Genetics Final

Use of PCR for cloning

After multiple cycles, almost all the DNA in the reaction will consist of copies amplified between the primers. These can be inserted into vectors for cloning for use as probes, sequencing etc. Although the 3' end of the primers must provide bases that pair with the target, a common practice is to add extra bases at the 5' 'beginning' of each primer that creates a restriction site after amplification. This is useful in 'directional' cloning or in combining different fragments later on.

cell theory

All cells come from pre-existing cells

Wheat originates from similar species that are 2N, to create 4N and 6N (or X) amphidiploids.

All of these have 7 chromosomes per set (X = 7). T is for Triticum, Ae for Aegelops and H for Hordeum, more commonly referred to as barley, another related cereal grain.

H^2 of IQ

All studies suggest that there is a genetic component, ie, that differences in genotypes affect IQ as measured by standardized tests. This does not mean that environment has no role, or that gene X environment effects might be just as, or more important ! Cyril Burt, was the first to use ID twins reared apart in 1943 to show that IQ has a strong genetic component. However, questions have come up concerning much of his data that was published after the first 10 pairs. In any case, his data fairly well align with other studies concerning correlation of relationship to IQ scores.

What kingdoms use DNA replication?

All three kingdoms: eukaryotes, prokaryotes, and archea

How to write defective alleles

Alleles with a minus superscript are defective: a-, b- lex-, etc.

How to write wild-type alleles

Alleles with a plus superscript are normal or 'wild-type'. a+, b+, lex+, etc.

Prosequencing

Allows thousands of small fragments to be sequenced simultaneously. Each DNA fragment is captured on a bead that goes into a tiny well and bases added are determined by a detector for each well.

Gossypium hirsutum, upland cotton, is an allopolyploid/amphidiploid species as well

Although several diploid species of cotton are grown commercially, most of the cotton grown in the US is a natural doubled haploid of a cross between 'old world cotton' and 'new world cotton'.

Alu elements are common in us and our relatives

Alu elements, named for the fact that they include targets for the restriction endonuclease from Arthrobacter luteus (AGCT) are an example of SINEs (short interspersed nuclear elements). They make up about 5% of the human genome (500,000 - 1 million copies).

Hemophilia

An X-linked recessive disorder in which blood fails to clot properly, leading to excessive bleeding if injured.

reverse transcriptase

An enzyme encoded by some certain viruses (retroviruses) that uses RNA as a template for DNA synthesis.

cytochrome oxidase

An enzyme present in particularly high concentrations in the mitochondria of dual-opponent color cells of the visual cortex

DNA helicase

An enzyme that unwinds the DNA double helix during DNA replication

Mice imprinting example

Another imprint example showing the presumed reason for imprinting and why nuclear transfer to an enucleated egg may be a problem. Igf = insulin growth factor.

null allele

Any genes that are are missing are essentially null alleles; if a large segment is lost, there is likely to be a recessive allele on the homologous chromosome so there may be a visible phenotypic effect in heterozygotes.

Pyrolysine (Pyl)

Around 2000, pyrolysine (Pyl) was discovered. Pyl is only found in some archaebacteria, especially those that are methanogenic (methionine producing). In this case, the tRNA that carries Pyl competes with the release factor the binds to the stop codon UAG. Which one will be produced most likely depends on the needs of the organism under certain conditions.

tryptophan operon

As opposed to the Lac operon where the presence of lactose induces activity to break down lactose, the presence of a biosynthetic endproduct such as an amino acid represses transcription of the long polycistronic mRNA. Here, the 'distant' trpR gene makes a co-repressor that binds to the operator (O) to prevent transcription only if it is first bound to tryptophan.

disomics n

Aspergillus nidulans can occasionally form diploids and then break down into haploids with the loss of chromosomes. In some cases a few or one extra chromosome may be present. This can help to identify genes that are on the same chromosome.

Beginning and end of introns

At the 5' end of an intron (beginning) there is GU and at the 3' end there is a highly conserved AG

BLAST search for HMGR

BLAST search shows areas suited for primers for amplifying HMGR segments, in this case by comparing rice to human sequences. At the time this BLAST search was made, there were only a few known HMGR DNA sequences available; now there are many. "Degenerate" primers can be made where a mix of bases can be added rather than a single base when that site of the primer is being added chemically. This will however lower effective primer concentration and specificity.

How Sickle Cell Occurs

Back in the 1950's Linus Pauling and colleagues discovered that sickle cell was a result of a single amino acid difference in the beta chain of adult hemoglobin. Normal adult hemoglobin is HbA and Sickle cell is HbS

Penicillin counterselection

Bacteria is grown in minimal media and then penicillin is added. The penicillin kills dividing bacteria, so if nutrient is missing that causes the bacteria to not be able to divide, it survives. Basically, the penicillin kills all non-mutant bacteria. Penicillinase is then added to the media to degrade the remaining penicillin. Then the surviving bacteria are moved to minimal media plate + a certain nutrient, to see what the mutant need to divide and to see where a metabolic block is occurring.

BACs and YACs

Bacterial artificial chromosome (BACs) and yeast artificial chromosomes (YACs) are vectors that allow the construction of recombinant DNA molecules with very large inserts of foreign DNA (hundreds to thousands of kb).

Bacterial Transposons

Bacterial transposons are 'composite elements' with Insertion elements at each end, usually carrying along a gene for antibiotic resistance between. TN movement is rare, in the case of IS10R being confined to DNA replication as a result of DNA methylation at 'dam' sites (-G^m ATC). Generally, only one of the IS elements is functional, but the matching ends allow the whole unit to transfer.

Drosophila salivary gland chromosomes

Banding was seen in these 'giant' chromosomes due to the fact that they are polytene as a result of numerous DNA replications without mitosis or meiosis, even though the homologues are paired

Top of tRNA

Bases are removed at the top and replaced with CCA on every tRNA

Bayes' Theorem

Bayes theorem allows determining which of various alternative hypothesis is more likely correct given a specific outcome. A complete set of mutually exclusive outcomes is required to calculate the probability. For example if a coin is tossed a number of times and all tosses come up heads (the 'event' in the above formula), when do you begin to suspect it is a 2 headed coin and when might you be 95% certain this was the case?

Where do MutH and MutS get their names from?

Because if they are defective, large amounts of mutations occur

Why was this still hard to believe?

Because it was hard to prove that there was no contamination on each plate. Or, if some protein got left behind along with DNA making it not possible to tell what was being read.

Why was it assumed that proteins carried genetic information?

Because proteins are much more complex structures than DNA. Proteins have over 20 different building blocks and multiple structures, while DNA only has 4 building blocks. It was assumed that 'only protein' carried enough information to make a new copy of itself, a feature critical for genetic information.

Why is mRNA in eukaryotes shorter than the original DNA template?

Because the entire gene is transcribed and introns are spliced out

Why is 5-bromouracil a mutagen?

Because the keto form acts as a T analog and the enol form acts as a C analog.

Why were there still skeptics?

Because these experiments were done on prokaryotes, and not eukaryotes.

Beginning and end of protein

Beginning is amino terminal and end is carboxy terminal, neither involved in a peptide bond.

What did Van Beneden describe and when did he do it?

Beneden observed meiosis of ascaris in 1883 provided drawing of the process

DNA fingerprintsvia Jeffries' probes from repeats with VNTRs*

Blood or semen from a crime scene has been used to identify the perpetrator in many cases. On the left we see that this VNTR/Restriction digestion pattern was identical to suspect #1 The case on the right was to confirm whether Father 1 or 2 could be the father of the child (lane C).

Brachyury

Brachy gene is lethal in mice if it is homozygous. The gene is part of a transcription factor in the T-box and is required to establish the anterior/posterior axis and is expressed in the intercell mast of blastocyst. If defective fetuses will most likely not survive.

Scientific Significance

By statistical convention, we use the 0.05 probability level as our critical value. If the calculated chi-square value is less than the 0 .05 value, we accept the hypothesis. Here we accept the hypothesis that the genes are assorting independently. Values of <5% due to chance are often said to be 'significant' while a less than 1% chance of getting the observed data if the hypothesis is actually correct is referred to as 'highly significant'.

Deamination example

C deamination to U -Examples in plant mitochondria and human nuclear encoded proteins •CGG to UGG, ACG to AUG (start), CAG to UAG all known

Why isn't caffeine a mutagen?

C is caffeine and it is a purine analog (it mimics the effects of methylxanthine, a natural purine, to affect serotonin in neurons, especially in the brain to stimulate 'alertness'). If has been widely tested form mutagenicity, but generally is not. Some studies suggest it may interfere with DNA repair systems, but if it prevents a type called error-prone, mutations decrease.

If the third base of an anticodon is a I (inosine, a modified A) it can pair with...

C, U, or A

CCG-1 and Mfa-1

CCG-1 and Mfa-1 are genes that make pheromones in mating type A and a, respectively that allow the two mating types to attract each other and fuse leading to .

protein degradation

Can be degraded when not needed or non-functional

Enzyme

Catalyst that lowers the energy of activation for a reaction to occur. An easier way of thinking about it is they are like magnets for the interacting molecules and they are going to break one apart.

Argonaute

Catalytic subunit of the RISC complex of the RNAi machinery. Responsible for the cutting (or "slicing") activity of RISC that destroys target mRNAs.

DNA lyase

Catalyzes the excision of the damaged pyrimidines and purines from ring saturation or opening from the DNA backbone.

Molecular basis for Achondroplasias

Caused by ACAN gene which is an aggregation condroutant sulfate that has varying splicing sites in tissues. in humans, the gene is fiberblast growth factor receptor which is critical for bone formation.

Examples of direct acting chemicals

Causes mispairing during replication

Pellagra

Causes skin damage and leads to mental situations, seems to run in families. However, this is actually a vitamin deficiency. So, if the whole family was eating Mom's cooking, they would all have Pellagra. Environmental rather than genetic effect.

CDC genes

Cdc genes code for proteins called cyclins, cyclin-dependent kinases (cdks) and phophatases. As indicated, a CDK with its cyclin combine to phosphorylate and thus 'activate' or 'deactivate' other specific target proteins, typically transcription factors but also proteins that destabilize the nuclear membrane. Phosphatases remove phosphates, thus altering or restoring the activity.

T cells

Cells created in the thymus that produce substances that attack infected cells in the body. assist and are also involved in tissue compatibility

adaptive peaks

Certain combinations of alleles from different genes may optimize fitness. It may be necessary to pass through intermediates with lower 'w' to combine the optimal alleles, especially if some detrimental genes are closely linked to the 'good' alleles. For example, if AbC and aBc are 'pretty good' but ABC would be better, it may be difficult to get to the optimal genotype.

Polyploidy

Changes in the number of whole sets of chromosomes •Polyploids may be 3N, 4N, 6N etc.

Erwin Chargaff (1947)

Chargaff's rules. Used DNA from a variety of different species and noted that the percent adenine and thymine were practically equal (purines), and that the percent of guanine and cytosine were basically equal (pyrimidines).

Plant defense enzymes and proteins

Chitinases B-glucanases Ribosome inactivating proteins Antimicrobial proteins

ChIP-Seq

Chromatin Immunoprecipitation combined with direct sequencing of precipitated DNA

Leptonema

Chromosomes appear as long, single threads, unassociated with one another

bithorax complex

Cluster of three homeotic genes in fruit flies that influences the adult fly's posterior thoracic and abdominal segments.

How common are competent bacteria?

Competent cells are rare under most conditions, as is uptake of DNA, so only a small fraction of a population is transformed.

Chemical Mutagen

Compounds that can be used to increase the rate of mutation

consensus sequence

Comprises the most commonly encountered nucleotides found at a specific location in DNA or RNA.

Painted chromosomes

Computer-assisted spread of fluorescent tags has shown for example that chromosomes occupy territories in the interphase nucleus, and that pairing of homologues end to end prior to formation of the synaptinemal complex (at least in C. elegans).

Examples of post cutting changes

Conversion of Hbb S allele to HbbA allele in human pluripotent stem cells - similar for SCIDs and clotting factor 8 defects Creation of a 'new' R gene in rice to counter a specific TAL effector; ie, change a promoter sequence somewhat Engineering adenovirus for use in gene therapy Phytase knockin expression in ENVIRO pigs, allows release of P from phytates Gene Knockouts in many species

RNA-seq

Converting the mRNAs in a sample to cDNA and then sequencing allows 'counting' the number of copies that were present and can detect alternately spliced messages. The technique has greatly enhanced 'transcriptomics' since all mRNAs present can be detected and quantified.

When are recessive mutations seen?

Could take more than one more generation to detect

Cre-lox notes

Cre is a site-specific recombinase protein that recognizes two flanking sequences called lox (loxP sites), which is locus of crossover. Lox recognizes 13 base pair inverted repeat flanking an asymmetric 8 base pair guide and two cre molecules bind to each lox, causing a crossover.

HLA genes

Critical in recognition of self and transplants of hearts, kidneys, etc. have many different alleles. An individual will reject any tissue containing an allele he or she does not have.

restriction nucleases

Cut DNA at specific internal sites -'protect' bacteria from foreign DNA -Can be 4, 6 or rarely 8 base sites

Practical examples of selection Insecticide resistant insects

DDT; 1908, no arthropods resistant: 1980 over 480 species BT resistance in several Lepidopteran species (earworms, bullworms); use of refuges of non BT crop plants is required for farmers Assumes that resistance is recessive and will be detrimental in the absence of BT.

Fluorescent in situ hybridization (FISH)

DNA Probes with a fluorescent tag attached can be hybridized to DNA stuck to a slide and then detected with a microscope equipped with fluorescent optics.

leucine zipper

DNA binding domain with a basic region that contains about 30 amino acids and is rich in arginine and lysine

Transcription process

DNA dependent RNA polymerase moves along the DNA strand unwinding it and uses RNA bases to make a complement strand to the template strand of the DNA. After it passes through the DNA, the newly formed RNA strand is released as mRNA (or the sense strand). Same as sense strand in DNA, except U's replace T's.

What protects the single strand of DNA when it unwinds?

DNA single strand binding proteins

southern blots use for

DNA/DNA hybridization

Creation and repair of AP sites

Damaged or wrongly pairs bases somehow have to be removed from the DNA. To do this, an enzyme called DNA glycosylase detaches the phosphate from the DNA backbone and detaches the damaged base. There are many types of DNA glycosylase specialized for each base pairing. This creates an AP site (A-Purinic or A-Pyrimidinic). AP endonuclease then cuts the DNA on one side or the other on the missing base. Then, with the help of an exonuclease the bases surrounding the AP site can be removed and repaired by DNA polymerase and DNA ligase.

deletions in tumor suppressor genes

Deletions in tumor suppressor genes often lead to a psueodominant situation, in that if the other copy of the same gene becomes defective in a somatic cell, cell division does not stop. Deletions of the imprinting region on chromosome 15 can lead to Prader Willi or Angelman syndromes when combined with the inactive allele that was silenced by genomic imprinting.

Southwesterns

Detecting DNA & protein interactions -These are often done using gel-shift assays, where an interaction decreases mobility of the RNA or DNA fragment -Allows determination of transcription factors and their binding sites for example

RFLPs (restriction fragment length polymorphisms)

Differences in DNA sequence on homologous chromosomes that can result in different patterns of restriction fragment lengths (DNA segments resulting from treatment with restriction enzymes).

Niacin biosynthesis pathway experiment

Discovered that in neurosporra, single gene mutants correspond to one missing enzyme rather a genetic block (like PKU).

Bayes Theorem Formula

E represents an outcome or event that has occurred Hi represents one member of a set of hypothesis that could have led to the event

Pheobus Levene (1909-1929)

Each nucleotide is a 3-phosphorus attached to a sugar attached to a base. Found that these were the building blocks of nucleic acid. Also credited for finding ribose in RNA and deoxyribose in DNA.

Two forms of each nucleotide

Each of the bases can exist in two forms by rearranging the double bonds or added hydrogen bonds. The rare form causes a pyrimidine to pair with the wrong purine, and vice versa. This always causes a transition mutation.

Sex determination process in humans

Early in embryology, all fetuses develop ovotestes, Mullerian ducts and Wolffian ducts The ovotestes can become either testes or ovaries The Mullerian ducts are necessary for internal female components such as oviducts and the uterus The Wolffian ducts develop into the prostate, seminal vesicles and vas deferens

Gateway vectors

Easy way to transfer a cloned gene into another cell with built in sequences

Chi-square example

Enter the Chi-Square table at df = 3 and we see the probability of our chi-square value is right at 0.90. That means that there is about a 90% chance of getting a deviation this large by chance would occur about 90% of the time.

DNA polymerase

Enzyme involved in DNA replication that joins individual nucleotides to produce a DNA molecule

DNA methyl transferase (DNMT)

Enzyme that catalyzes the addition of methyl groups to bases of DNA. Functions to prevent restriction endonuclease from cutting up cellular DNA.

DNA ligase

Enzyme that seals the single-strand DNA fragments on the lagging strand

Eukaryotic promoters

Eukaryotes have different RNA polymerases and promoters for the three types of RNA; Pol I for large RNAs like rRNA, Pol II for mRNA and Pol III for small RNAs like tRNA

Heterochromatin

Eukaryotic chromatin that remains highly compacted during interphase and is generally not transcribed.

eukaryotic ribosome vs. prokaryotic ribosome

Eukaryotic ribosomes are larger and an extra small rRNA fragment

Gene frequencies vary!

Even though the same genes and common alleles are present, there are often differences in the frequencies at which the alleles are found when specific groups or populations are analyzed.

How antibody gene splicing is accomplished

Every V region has a preceding repeated heptamer and nonomer with a 12 or 23 spacer between. The same sequence occurs in reverse after the J regions. Enzymes RAG1 and RAG2 can bind the hairpins that form and splice out the DNA in between. In H chain genes, the J's only have the 23 bp spacer and the D's only have the 12 bp spacer leading to a VDJ joint. If the first attempt to make a full length chain fails, a second attempt is made from the other gene in the diploid cell: once productive, that B cell only expresses one antibody gene. Initial expression produces IgM which is attached to the outer cell surface. After activation, switching will lead to secretion of IgG, IgA etc. forms of the same antibody.

Constitutive splicing

Every intron is spliced out and every exon is spliced in

Segment polarity genes examples

Examples include engrailed, hedgehog, frizzled and wingless that act as morphogens and act to create a border between stripes. They are expressed when cell formation is occurring. (div 13). Some encode signals, others receptors.

How did they find live smooth bacteria in these mice if it was killed when injected?

Experiment showed that avirulent 'rough' bacteria could be converted to smooth virulent (cause pnemonia in mice) by some agent from killed smooth strains: the change was 'inherited' so it involved genetic information

pre-rRNA processing

External and Internal Transcribed spacers (ETS/ITS) are cleaved out of pre-rRNAs by snoRNAs just like introns and extrons in mRNA

What happens if thymine dimer aren't fixed?

Failure to make one of several enzymes that function to cut thymine dimers from the DNA and patch the gap have a very high risk of getting skin cancer from exposure to sunlight.

What did Fleming discover and what year did he discover it?

Fleming described mitosis in 1882 from observations using salamanders. He saw doubled chromatids and suggested each nucleus came from a prior nucleus.

Alternate outcomes of floxing

Floxing creates a double strand break, which can be repaired in two ways. The first being non-homologous end joining (NHEJ), which can result in frameshift mutations. The second way is homologous DNA repair (HDR).

Riboswitches

Folded RNAs that act as switches regulating protein synthesis in response to environmental conditions

Mendel's 'worst' F2 single gene ratio

For pod color, the legend is G_ green, gg yellow. When Mendel crossed a green podded plant to a yellow, ll the progeny were green. Self pollination gave the F2 ratio 428 green:152 yellow

Poisson Distribution

For rare events the Poission is much easier to use than the binomial. It asks what is the probability of seeing exactly X outcomes when we know the average rate.

joint occurrence

For the joint occurrence of two events we will have to add however if they can occur together, we need to subtract the joint occurrence once.

Maintenance of the permanent translocation heterozygote Oe. biennis strain suaveolens Grado.

Free segregation of chromosomes and homologous recombination is suppressed in the complete permanent translocation heterozygote between the haploid Renner complexes Galbicans (yellow) and Gflavens (orange). Gametophytic lethal factors repress germination of Galbicans pollen, and sporophytic lethal factors eliminate homozygous Gflavens·Gflavens offspring in F1. Referring to the parental generation, identical offspring are produced in F1.

If the third base of an anticodon is a C, it can pair with...

G

Rate of transcription for purines vs pyrimidines

G-C pairings take longer to synthesize compared to A-T bases.

Steps of the cell cycle

G1, S, G2, M

What does elongation require for every amino acid added?

GTP Another GTP is required to 'ratchet' the mRNA and growing polypeptide attached to the last tRNA used to the P site after peptide bond formation which is done by a 'peptidyl synthase ribozyme' that is part of the large subunit of the ribosome.

Gene segregation in a fertile tetraploid

Gene segregation in a fertile tetraploid is affected by its distance from the centromere

Regulation of cyclins

Genes such as the Rb (retinoblastoma, a gene that is named for its association with cancer of the retina in humans) are considered negative regulators of cell division, which accounts for the reason that they are classified as 'tumor suppressor' genes. (ie., if there is no functional Rb protein, cell division does not stop).

Homeotic genes

Genes that determine basic features of where a body part is defects lead to misplaced body parts

IPTG

Gratuitous inducer of lac operon: inactivates repressor but is not broken down by β-galactosidase

What does this infer?

Guanine and cytosine have a stronger bond than adenine and thymine, meaning then when introduced to heat, adenine and thymine will fall apart faster.

CRISPR/Cas9 components

HNH and RuvC are two (of six) domains in the Cas) nuclease. One cuts the RNA complemented strand of DNA and the other the other strand. Another Identifies the 3 base PAM to guide cutting site, PAM varies in different bacteria. The PAM sequence an be 2-6 bases and tells the nuclease where to cut. First use in mammals 2013; can use Cas 9 defective to bind DNA and prevent transcription etc. Also, binding efficeincy can be reduced if 5mC is present at target

HRP genes

HRP genes can trigger hepersensitive response, so could be 'anti-infection' in resistant hosts.

Finding optimal doses for discovering mutants

Have to balance mutations and death while administering certain does to find the optimal dose

Aneuploidy

Having extra or missing Individual chromosomes

Mendel reciprocal crosses

He also made all the reciprocal crosses to verify that it did not matter whether the alleles came from the egg or pollen, ie., tt (dwarf) female X TT (tall) male gave all Tt (tall) progeny The F2 generation in this case gave 787 Tall : 277 Dwarf. Mendel concluded this was a 3:1 phenotypic ratio resulting from random combination of T and t gametes.

Mendel selfing the F2 generation

He used one more generation of selfing to show that the F2 genotypic ratio was 1 TT: 2 Tt: 1 tt , ie, that 2 of 3 tall F2 plants were heterozygous while the other 1/3rd was true breeding (homozygous).

Tissue specific knockouts

Hepatic nuclear factor 4a is a transcription factor that regulates genes involved in mature onset diabetes in youngsters; Cre here is driven by a liver promoter

Microarray example

Here DNA from many defined genes is placed on a glass slide (in paired spots) where it is fixed, and then hybridized to labeled first strand cDNA from all the mRNA in control and treatment samples labeled with different colored dyes. If the dyes 'balance out', the amount of mRNA for each sample was the same (yellow in this case).

Models for recruiting target specific histone modifiers to lower gene expression via de-acetylation.

Here deacetylases are being recruited to help lower expression. Here the URS stands for upstream repressor sequence

lack of penetrance example

Here we see a case of what is considered a dominant gene for ploydactyly which did not appear in several individuals but did in their progeny. In some of these cases, X-rays showed extra bones, but not the development of the extra digit.

Is it one gene?

Here we see the results of a single gene spore color mutant, but if a Thi+ is crossed to a Thi- the resulting spores would also show a 1 to 1 ratio for thiamin auxotrophy if a single gene is segregating. Beadle and Tatum verified that each auxotroph found behaved as a single gene mutation and also determined which auxotrophs for a particular compound were in the same or different genes.

•1 in 700 babies born has trisomy 21. •If 1400 babies are born in a hospital in one year, what are the odds that X = 0, 1, 2 or 5 will have trisomy 21?

Here, m will be 2, since we expect 2 in 1400.

What did Hertwig describe and when did he do it?

Hertwig observed and provided illustrations of meiosis in sea urchins in 1876

How is rRNA conserved?

Highly conserved, and can even be used to distinguish kingdoms

Histone conservation

Histone genes and protein sequences are among the most conserved known across eukaryotic species. The number of interactions required between the 8 subunits of a histone ball and providing a surface for DNA interactions leave little room for change.

Altering histones

Histone methylation, as shown at the bottom is another mechanism for altering histones; the acetylation is by Histone Acetyl Transferase (HAT) and removal by histone deacetylases (HDAC); methylation is by histone methyl transferases (HMT). Acetylation 'opens' while methylation condenses the nucleosomes.

DNA ligase

Hook DNA fragments together -Requires ATP - can combine blunt ends, but sticky ends are an advantage because base pairs find each other easily

Micronuclei test

Human and mouse tissue culture lines (or bone marrow in vivo) are used in tests to reveal agents that cause breaks in chromosomes. The fragments without a centromere do not segregate to the poles in mitosis, resulting in the formation of 'micronuclei' as seen on the right.

Plant Cell Synaptonemal Complex

I assume that the colors were added artificially to distinguish each chromosome since the same proteins would be present in all paired chromosomes.

For II-1

II-1 is normal: she must be AA or Aa Two of 3. NORMAL progeny in this case can be expected to be heterozygous !

Linkage Drag and Linkage Disequilibrium

If 'A' is strongly selected, closely linked 'b' may be carried along, even if it is slightly detrimental. When population analysis shows f(AB), f(aB), and f(ab) are not as predicted (should be 'equilibrated' to allele frequencies over time) this linkage disequilibrium suggests a nearby strongly selected allele.

Probabilities of simultaneous events

If A and B cant happen together, P(AB) will = 0

Chance that HD is passed on

If a parent has HD, the odds a child will have that allele start out at 50%, but decrease the longer he/she lives without symptoms

Corollary of Hardy-Weinberg Equilibrium

If mating occurs at random, not only will the allele frequencies remain constant, so will the genotypic frequencies.

Use of PCR to amplify segments of amino acids

If the amino acid sequence is available a segment of the gene can be PCR amplified by using 'degenerate' primers designed to match regions with low codon degeneracy.

Trinomial

If there are 3 possible outcomes, such as red, roan or white, all we need to do is add another term.

Cre-lox catalyzed rearrangements

If you flox a gene with both loxP's facing towards the middle, you can create an inversion after crossover. If you have them both facing the same way, you then you can remove/delete the gene. If you have two lox-Ps on two different chromosomes, you can create translocation.

Histidine and strep-tag

If you have 6 histidines or a strep-tag at one end of a protein you can use that magnetic beads to bind to these tags and pull the protein out of the solution in order to purify the protein.

site-directed mutagenesis (SDM)

If you have a DNA fragment cloned in bacterial plasmid, you can build primers to allow the change of one or two specific codons.

Huntington's disease

If you have more than 35 CAG codons in the coding region, then you're liable to get Huntington's disease.

How specific codons were discovered to code for specific amino acids.

In 1960s, after it was discovered that you could get ribosomes to function, if GTP rather ATP was present, three different labs were credited for finding genetic code and they shared a nobel prize. The first successful experiment done was making poly-U messages. Poly-U was added to the translation and produced the protein polyphenylalanine. If the codes are three bases long, then the code for phenylalanine is UUU. The same experiment was done with poly-C and poly-A, and the proteins polyproline and polylysine were produced. The next experiments were done with alternating bases which would give two code words and proteins with alternating amino acids. They then found you could make amino acid with one codon. Even if there wasn't a start codon, an amino acid could be seen stuck on the tRNA. For UAA, UAG, and UGA, there were no amino acids stuck to the tRNA. They referred to these as nonsense codons. Later known to be stop codons.

Sex determination pathway in Drosophila

In Drosophila, the Y chromosome does not have a role in sex determination, but is essential for sperm production. The X/A ratio triggers male and female development via the cascade of differential splicing events

Genetic heterogeneity for OI

In OI, it is not only the ColA1 and ColA2 genes that can cause the defect, but also the 32 or so other genes that trim the ends and make the modified amino acids.

tetratype (TT)

In an ascus, the occurrence of both types of parentals and both types of recombinants among the spores.

Termination of translation in prokaryotes

In bacteria UAA and UAG are recognized by a release factor (RF1). There is no tRNA, instead the release factor, when either of these two stop codons enters the A site, binds to the stop codon and triggers the peptidyl synthase to fire one more time, which hooks a water instead of another amino acid that then releases the growing polypeptide chain. UGA is recognized by bacteria by RF2.

Components of prokaryotic ribosome

In bacteria, the two ribosomal subunits of a 70s ribosome can be taken apart and there is a 50s subunit and 30s subunit. If you take the 50s subunit apart, you see that it has a large rRNA a small hairpin.

Chloroplast genome

In contrast to the variability seen in plant mtDNA, the ctDNA is generally around 121 Kb. It has two copies of the rDNA genes, a set of tRNA genes and also codes for proteins that are part of complexes involved in energy capture for CO2 fixation. As in mitochondria, many key components of the same complexes are coded by nuclear genes. One example is RUBISCO, the enzyme used to fix carbon from the atmosphere and said to be the most abundant protein on earth. The large subinit is coded by ctDNA and the small is nuclear.

Mendel results from monohybrid crosses

In each cross, the F1 progeny all resembled one parent, defining the dominant version of the character (later attributed to the dominant allele), but the alternate phenotype (recessive) made up 1/4th of the progeny in the F2 generation from self pollinated F1 plants. Mendel recognized the significance of this ratio before statistical tests were available.

Gymnosperm mitochondria

In gymnosperm plants like loblolly pine, mitochondria are paternally inherited but chloroplasts show maternal transmission.

The use of cytoplasmic male sterility in plant breeding

In many crops, making crosses can be difficult, or in the case of maize, the expense of hiring 'detasselers' made the proposition of using male sterile lines as females to create hybrids with the associated hybrid vigor, led seed companies to the use of a scheme like that shown on the right to produce hybrid seed for sale to farmers.

Use of CMS in naturally self-pollinating plants: Rf genes restore fertility

In naturally self pollinating crops such as sorghum and canola as shown here a '3-line' scheme is used. The A line which is male sterile [S] and rf/rf (does not restore fertility), is backcrossed continually using pollen from the B line which is also rf/rf but has fertile [F] cytoplasm. The B line is maintained by selfing. Thus the A and B line are genetically the same for nuclear genes. The R or restorer line, selected for good general combining ability and homozygosity for Rf/Rf is then used to create hybrid seed, with the seed collected from the male sterile female parent.

Transposon silencing

In plants components of the RNAi system help to prevent expression of the transposase and thus prevent major genome disruption. Since TNs often have foldback regions they can be 'diced' and on some argonaut proteins RDR^, an RNA-dependent RNA polymerase can make multiple copies which can then associate with complementary DNA sequences to guide histone and DNA methylation. PIWIs from short non protein coding genes in Drosophila and animals form piRNAs that interact with specific argonauts and appear to do the same thing.

methylation in prokaryotes

In prokaryotes, methyl adenine is common rather than 5mC.

Trisomic plants

In some plants such as Jimson weed and tomato, lines that have trisomy for each of the 12 chromosomes can be identified (by an expert) based on phenotype. The lines can be maintained by crossing to a normal and selection in each generation. Typically, the extra chromosome passes through the egg and not the pollen. Also having one dominant allele is usually enough to see the dominant phenotype for a gene on that chromosome.

chromosomal sex determination snakes and birds

In some snakes and all birds, females are heterogametic ZW and males are homogametic ZZ. The W is much smaller than the Z and has few genes.

independent assortment

Independent segregation of genes during the formation of gametes

Phenylketonuria (PKU)

Inherteted as autosomal recessive. Individuals who are homozygous for the defect in the phenyalanine hydrolase end up accumulating phenylketones. Results in severe retardation (can lose 1-2 IQ points per week during early development) and light skin because pathway to make melanin is blocked (if untreated).

Bacterial Insertion Sequences

Insertion sequences in E. coli were discovered in gal- operon mutants that were polar (ie, prevented all subsequent proteins from being made in a polycistronic mRNA) and were not reverted by acridine treatment. When used to create heteroduplex DNA, the mutant allele was larger than the normal. Structures were determined in the late 1970's. They all have short inverted repeats recognized by the transposase they encode and most create in-frame repeats at more or less random sites in the chromosome. There is about a 1 in 1, 000 to 1 in 10,000 chance for moving in each generation and a much lower chance for a precise excision.

Insulin formation

Insulin, a common hormone that is defective in people with diabetes, starts out as a longer protein and is secreted into the lumen of the ER. The signal sequence is then cleaved and is then folded and two other enzymes cut off one end of the protein. Two other bonds are formed so that the two remaining pieces stick together, resulting in the mature insulin. The first form of insulin in referred to as pre-pro-insulin, and when the signal is cut off it becomes pro-insulin, and the final product is insulin.

How they proved that DNA was ultimately the transformation agent

Introduced enzymes that degrade each of the compounds. If DNA was treated DNAase, then the ability to cause transformation of the bacteria went away. This did not happen if proteases were introduced, which broke down the proteins. Proteases also ensured that no protein was left behind with the DNA.

Chi-square

Involves categorical variables. Looks at 2 distributions of categorical data to see if they differ from each other.

For purines...

It is not true in some cases. ie UGG is Trp, but UGA is a stop codon and AUG is start but AUA is isoleucine

How mutagen killing curves can reveal the number of targets

It is possible to project back from the linear killing part of the curve to see the number of 'targets' (haploid nuclei) that were present.

tRNA activation

It takes high energy (ATP) to connect amino acid to the terminal A of a tRNA

Triploid turtles

John Bickham from the Wildlife Department at TAMU (at the time) found a turtle in the Amazon drainage where many were triploid or 2N/3N mozaics

Oilseed Rape

Just as the species is man made, so is the name of the cooking oil made from it, ie "Canola" which stands for Canadian Oil, since that is where the crop is primarily grown. While the original strains had high levels of erucic acid which is considered a heart hazard, breeding has dropped the level nearer 0.5%, well under the standard for food use, while also lowering the levels of saturated fats below other cooking oils. As with any oil, cooking at too high of a temperature can produce carcinogens.

Membrane location signals

Just like in the case that there is a signal for proteins that need to be transferred into the endoplasmic reticulum, there is also a second signal that leads them where they need to go. These usually do not get cut off. These are things that end up being membrane targeting and end up in the membrane.

Molecular basis for lethal white

KIT gene is an oncogene that is a cytokine self-surface repressor protein that interacts with the cytokine and triggers a phosphate signaling pathways going through stack proteins.

2020 human use

KO Nanos2 required for male fertility in mice, pigs goats, etc. : insert donor allogenic stem cells into testes: sperm are from the donor. Touted as a way to get herd improvement in areas where AI is not available or possible. RNA-targeting Cas9 (RCas9), to eliminate the toxic RNA and almost fully reverse symptoms in a mouse model of myotonic dystrophy (adult onset, Trinucelotide repeat with too many CUG repeats in the mRNA

polymerase chain reaction (PCR) 3 step version

Kerry Mullis won nobel prize for this discovery

Bacteriophage lambda

Lamda is about 47,000 bases long and is linear but has complementary single stranded tails (cos sites for cohesive ends). It also has an att (attachment) site for integration into the host chromosome between the bio and gal operons. Occasionally the integrated λ comes out incorrectly and carries along one of these genes creating for example a λdgal (λ-defective-gal) particle. When introduced into another host cell, this λdgal can integrate by a single crossover (recombination event) or via the att site to create an Hft (high frequency transducing) strain and can be used to test for complementation and dominance for example since these cells have 2 copies of the gal genes.

Discovery of conjugation Lederberg and Tatum (1946)

Lederberg and Tatum mixed two strains of E. coli, one with thr-, leu- and thi- auxotrophic requirements and the other with bio-, phe- and cys- defects. They found rare wild-type colonies, along with strains with new combinations of markers. They also showed that contact was required between the strains and that nothing in the growth medium could lead to the new genotypes (ie, transformation was not the basis for the change).

Budding defect mutations in yeast

Lee Hartwell received a Nobel prize for discovery of many cell division cycle (cdc) genes (about 70) that regulate cell division. Most were identified as temperature sensitive alleles (grow at 25, not at 37°C) . Each mutation prevented completion of the cell cycle, as observed by failure to complete the budding process in Saccharomyces cerevisiae. Double mutants helped reveal the order of function around the cycle. Many of the yeast genes have counterparts in higher organisms, including humans

Muller X-ray mutagen experiment results

Left: Each type of data point is from a different experimenter: up to 6Kr, the effect on producing a recessive lethal somewhere on the X chromosome was linear. Right: at higher doses (these are actually r X 10-3)chromosome breaks are induced in tissue culture cells; some require 2-hits to show the effect, so exhibit a non-linear dose response

Left arm of tRNA

Lefthand loop has a series of specific nucleotides that provide identification of the amino acid it carries.

How SOS repair is activated

Lesion in template strand halts synthesis of new strand. DNA polymerase resumes synthesis further down the strand leaving a single stranded gap. In E. coli, a protein called lexA inactivated and signals for SOS repair to occur.

Which three amino acids have 6 codons and are all used?

Leucine, Serine and Arginine

Chlamydomonas

Like yeast, haploid cells of opposite mating types (+ and -) in this case of the unicellular alga Chlamydomonas sp. fuse to form a diploid. They then usually (95%) undergo meiosis to form haploid vegetative spores that can produce gametes of each mating type. As algae, they have both mitochondria and chloroplasts. In the zygote, mitochondria from the + strain are destroyed as are chloroplasts from the - strain. Thus, unless something like UV treatment alters the normal situation, there is uniparental inheritance of the organelles, but it is only the ct+ DNA and mtDNA that is transmitted.

Linus Pauling sickle cell experiment

Linus Pauling and colleagues later able to get pure beta chains from sickle cell patients and also normal HbA, and subjected them to digestion with trypsin and chymotrypsin. These enzymes will cut wherever there is a lysine and arginine, or where there is a phenylalanine and tyrosine for the other. So, this cut the chains of the hemoglobin beta peptide from around 140 amino acids into small fragments. The 2-D electrophoresis showed that all of the fragments were the same except for one. This one fragment showed a single missense mutation that caused the hemoglobins to differ.

Slippage

Long repeats of nucleotides or codons can result in extra or not enough bases being coded for during DNA replication.

Trisomy 18 (Edwards Syndrome)

MR Rocker bottom feet Prominent occiput Clenched fists w/overlapping fingers Congenital heart disease Horseshoe kidneys IUGR/FTT 90% die by age 1

How to get around this?

Make a gene. This can be done because chemically adding and deleting bases. Then the gene can be transcribed and cyanogen bromide is used to cleave off the leader sequence to from a functional protein. This method wouldn't be efficient for really large genes.

shotgun cloning

Making a plasmid library of DNA fragments

DiGeorge Syndrome

Maldevelopment of 3 and 4 pharyngeal pouches, fascial dysmorphia, cardiac shunt, lack of T-cells, undeveloped paracortex

Protein editing

Many are made in a longer 'pre' form and edited

Specificity of proteins

Many are targeted to specific locations

coenocytic fungi

Many fungi are coenocytic, and even in some that have septae, the nuclei can migrate 'cell to cell'.

decorated secreted proteins

Many secreted proteins are glycoproteins that are said to be highly 'decorated' by having extensive and branched chains of attached sugars. Examples include mucins and blood type antigens.

Maternal effect PAR

Maternal effect PAR (protease activated receptor) proteins from C elegans to mouse help establish polarity in causing asymmetry according to spindle fiber attachment region with more smaller cells.

Types of proteins

May be enzymes, structural components, hormones etc.

Protein folding

May require chaperones to fold correctly

Mendel and true breeding

Mendel 'selfed' (self pollinated) plants displaying each character for several generations to verify they were true breeding (we can now say homozygous for the trait) before making crosses. Crosses between true breeding parents showed all F1 progeny in each of the crosses exactly resembled one parent.

Microtubules

Microtubules in the typical 9 sets of 3 arrangement as seen in animal cells: centrioles later form the basal bodies for flagella and cilia. Higher plant cells do not have a classic centrosome with centrioles but do have a microtubule organizing center to organize their microtubules and share some common 'organizing' proteins.

Neurospora crassa life cycle

Millions of asexual spores can be collected from a single tube after a short growth period. Crosses take about a month before mature spores are ready to germinate

Ames Test Example

Millions of his- Salmonella were plated on minimal medium where only his+ revertants can grow. Control on left shows the spontaneous reversion rate; the compound added to the tab on the right is clearly mutagenic. Different strains have different original mutations allowing transition-, transversion- and frameshift-inducing mutagens to be detected. Can pretreat with S9 fraction from livers of rats fed a compound that induces 'de-tox' enzymes that can create free radicals via normal metabolic steps.

unequal crossing over

Misalignment of the two DNA molecules during crossing over, resulting in one DNA molecule with an insertion and the other with a deletion

MAP kinase

Mitogen-activated protein kinase. Signaling molecule that is the final kinase in a three-kinase sequence called the MAP-kinase signaling module.

FISH detection of a deletion

Modern technology makes it much easier to screen for a deletion and can even be done prenatally. Here a green fluorescent probe for a specific gene only appears in one of the two homologous chromosomes.

Aptamers

Molecules that act as switch in riboswitches

TaqMan

Most popular method of quantitative PCR; two primers and one probe; probe has a fluorescent (reporter) dye on 5' end and a quencher molecule on 3' end; as long as probe is intact, fluorescence is quenched; during DNA synthesis, Taq polymerase cleaves the probe, releasing the dye

Muller X-ray mutagen experiment

Muller created the ClB technique using drosophila. C was a gene on the X chromosome that stood for crossover suppressor. This was dominant so a chromosome had it there was no crossing over. L was the recessive lethal on the X chromosome that could only survive in females. B was the bar eye mutation that in homozygous females would cause very narrow eyes. In heterozygous females had wide bar eyes, and heterozygous normal had normal kidney shaped eye. Muller started by x-raying males with varying doses and then tracked the X-chromosome that went through the sperm. He then selected wide-bar daughters from that cross, meaning they had one X from the bar ClB female and one X from the irradiated male. If the wide-bar female was crossed with a normal male, you could look for cases where there were absolutely no sons, because if the new recessive lethal on that cross-hatch x was present, the sons wouldn't survive. If the X from the female that started with the bar-eyed gene, there would be no sons because this was recessive lethal.

The 'forces' they identified include:

Mutation Migration Drift Selection

Adaptation/induced mutation theory

Mutations can occur only in the presence of a mutagen

Mutations effect on transcription

Mutations in promoter can effect the ability to make mRNA. Even in the leader region, mutations can remove the ability to make mRNA.

chromosomal mutation

Mutations that alter chromosome structure

revertant

Mutations that can be reversed i.e. point mutations

recessive mutation

Mutations that create a new allele recessive to the original

suppressor mutations

Mutations where a second change 'overcomes' a different mutation

dominant mutation

Mutations where the new allele is dominant

Two consecutive signals to get into the Ct thylakoid

N-terminal chloroplast signal sequence (red), followed immediately by a thylakoid signal sequence (orange).

•Would a population of 500 including 200 Type M blood, 200 type MN and 100 type N be in equilibrium? C2 tests can be used to measure 'goodness of fit'. -Here the degrees of freedom is (# of phenotypes-# of alleles) (3-1) so here= 1

No, does not follow p^2 AA : 2pq Aa : q^2 aa

SYBR Green

Non-specific intercalation into the minor groove of dsDNA, can be used in qPCR

goodness of fit

Not a percentage! X is in degrees of freedom

Notch wing Drosophila heterozygous for a deletion on the X chromosome

Notch gene encodes a receptor protein that extends through both sides of the cell membrane and which is capable of interacting with a ligand partner, such as the protein Delta, presented on the surface of a neighboring cell. This cell-cell interaction causes the cleavage of an intracellular region of the Notch protein, freeing it to move into the cytoplasm and triggering the activation of transcription factors within the cell's nucleus. When first discovered, the deletion also created a null allele for eye color giving the impression of a dominant gene for white eyes. Homozygous females or X^N Y males do not survive.

Bar eyes in Drosophila

Note that a 'position effect' is also present in that eyes of females with 3 copies on one chromosome and one on the other are narrower than the fly with 2 copies on each X chromosome. Males are either normal or have one of the Bar phenotypes.

Membrane spanning sequences making pores

Note that the N and C termini can be on either side of the membrane and that there can be multiple signals to embed a protein in a membrane which for example, may create a pore.

Origin of oilseed rape

Note the genome designations of the species that contributed: it is likely that direct AA by CC diploid species crosses are not possible

uniparental disomy

Offspring receives 2 copies of a chromosome from 1 parent and no copies from the other parent. In case of Prader-Willi and Angelman syndrome, Either can also rarely occur when both chromosomes in the fetus came from the same parent

blue-white screening with pUC plasmids

On a plate with XGAL in the medium, funtional b-galactosidase produces a blue pigment; thus, the white colonies are ones that have a disrupted Z gene in this host strain so should have foreign DNA inserts.

Competition between lysogeny and lysis in lambda

On entry of λ DNA into a host cell, left and right promoters (PL and PR) are recognized by host σ factor and RNA polymerase to read 2 genes, N and Cro. N codes for an antiterminator that allows longer messages that are translated to make the additional proteins CI, CII and CIII. CII, protected from host HflA protein by CIII, acts as a σ factor for PE, a promoter for establishment of lysogeny. This results in more CI protein being made. CI is the repressor of the lytic cycle. Cro protein stimulates "outward" expression of genes from PL and PR needed for lysis and lowers "inward" synthesis of CI mRNA by binding to OR3. OR3 is one segment of a 3-part operator (OR3-OR2- OR1) between PL and PR. CI binds preferentially to OR1, preventing outward transcription of lysis genes and enhancing its own synthesis from PM, a promoter for maintenance of lysogeny.

Receptor Tyrosine Kinases (RTKs)

On outside of membrane, there is a ligand binding site. When the ligand site is bound, there is action on the inside of the cell (phosphorylation/dephsphorylation cycles)

mutually exclusive exons

One of two exons is retained in mRNAs after splicing, but not both.

Binomial "at least one" example

P (at least 1) = 1-P(0)

Examples of generalized transduction

P1 of E. coli packages 90 KB or about 2% of the chromosome BS1 of B. subtilis packages 240 KB or about 10% of the chromosome P22 in S. typhimuriumpackages 41 KB or less than 1% of the chromosome

Plasmids as a vector examples

PBR322 pUCs

PRE 1 and 2

PRE 1 & 2 are pheromone receptors. The interactions trigger cassic G protein activation of cAMP and MKKK pathways leading to the actual steps require for mating in Neurospora. Deb- Belle Peterson In Biology does lots of this work.

Killer Paramecium

Paramecium micronuclei go through meiotic division and produce one functional nuclear genome. Then, if it mates with another for a long time, the cytoplasm changes. The presence of a bacterium does not kill the paramecia with K gene expressed but will kill k gene expressed paramecia.

Dupont-Pioneer targeted editing broken down

Partial ALS2 sequence with ALS-gRNA target site, protospacer adjacent motif (PAM) is boxed and proline codon (amino acid position 165) to be edited is underlined. (b) Partial sequence of the ssDNA oligo used as a repair DNA template; modified nucleotides are shown in red font and serine codon is underlined. (c) Wild type (left) and ALS2 edited (right) plants tested for resistance to chlorsulfuron (200 mg l−1); shown at 10 days after spraying.

Is conjugation always successful?

Partially successful most of the time. Conjugation is disrupted before it is complete most of the time, resulting in partial transfer of the HFR's genes.

pea plant characteristics

Peas have a 'perfect' flower, with both male and female reproductive organs; the flower is normally closed so that self fertilization occurs. Crosses are made by removing anthers before pollen is produced and introducing pollen from a different strain (variety). Each pea produced represents an independent fertilization. It was also important that they are diploid, ie., have two sets of chromosomes/cell

age of onset

Person's age when he or she develops or exhibits symptoms of a disorder.

calf intestinal alkaline phosphatase (CIAP)

Phosphatases that prevent ligation

frameshift mutation

Point mutations that add or subtract a base create

Missence point mutation

Point mutations that change a codon to a codon for a different amino acid (often nonsynomymous)

samesense (silent) mutation

Point mutations that change a codon to another for the same amino acid

Proteins

Polymers of amino acids

Drosha and Pasha (DGCR8)

Prepare the functional micro RNA for export where they can affect expression of many genes via base-sequence homology

Tsix gene

Prevents X chromosome inactivation

The DNA in human (and other eukaryotes) mitochondria is circular and not condensed with histones

Properties of the organelle have suggested that they likely arose from independent endosymbiotic prokaryotic organisms that have lost much of their genetic information. Although there are no histones, TFAM (transcription factor A, mitochondria binds the DNA to form nucleoids. It is critical for transcription and replication. It is coded by a nuclear gene on chromosome 10 in humans. ( Defects in TFAM are associated with Parkinsons and Alzheimers.)

How this problem is avoided

Protein called NusA is able to displace the sigma factor and ultimately control the rate of transcription to prevent rapid transcription.

Plant and fungal mtDNA

Quite variable in size among species, even relatives Fungi mtDNAs range from 17.6 Kb (S. pombe) to 175 Kb (Agaricus) Sometimes can be cut into two sub-genomic circles by a single crossover They do include introns and non-coding regions Some transcript processing involves ribozymes for self splicing

RNAi

RNA interference; injecting double stranded RNA into a cell turns off expression of a gene with the same sequence as the RNA

siRNAs (small interfering RNAs)

RNAs of similar size and functions as miRNAs that inhibit gene expression.

how antibiotic resistance happens

RTFs (resistance transfer factors) pass on resistant genes to susceptible bacteria population via conjugation

oncogene examples

Ras, Raf, MEK, ERK

Effects of ROS

Reactive oxygen can species damage DNA, membranes, enzymes etc. as well as trigger apoptosis. Singlet oxygen is created in chloroplasts where CO2 fixation from capture of suns energy is occurring. The plant makes protective carotenoids, tocopherals and quinones for absorbing free radicals. H2O2, induction also has a role in strengthening host cell walls. Activated NADPH oxidases, in plants referred to as respiratory burst oxidase homologs (RBOHs), contribute to formation of ROS. In Arabidopsis when two RBOH genes are inactive, there is less PCD.

Tautomer

Rearrangement of hydrogen bonds within the base ring structures of each base occur spontaneously and each pairs with the wrong purine or pyrimidine partner (transitions may result)

Rec A is a critical protein in recombination.

Rec A mutants have almost no recombination, hence the basis for the name. As we have seen in post-replication repair, this protein is functional in finding a complementing partner for a single strand of DNA and displacing the original partner if necessary. It can even displace one strand of a circular plasmid if a complementary strand is added to the mix in a test tube system.

Arber, Smith, and Nathans (1978)

Received a Nobel prize in 1978 for the discovery of restriction endonucleases and their site-specificity. Those described here are 'type II' which recognize and cleave within specific base sequences.

Recessive lethals in heterozygotes

Recessive lethals generally show no effect in heterozygotes

Red and green opsin

Red and green opsin (color receptor) proteins differ by only 15 amino acids and the genes are practically adjacent on the X, suggesting that unequal crossing over can occur to give rise to the high frequency of mutant alleles that are known.

Selenocysteine (Sec)

Referred to as the 21st amino acid. In 1986, selenocysteine was recognized is actually put into the protein using a UGA stop codon with a special mechanism using a tRNA. The tRNA is a serine cognant tRNA. In E. coli there is cell A, B, C, and D. Cell C is the one that codes for the serene tRNA. Cell A and D convert the serine to selenocysteine while it is still on the tRNA. Then cell B replaces the elongation factor Tu. The mechanism involves a hairpin structure called selenocysteine insertion sequence (SECIS) that forms a 60 nucleotide long stem loop. It is found in bacteria soon after the stop codon. In eukaryotes it is found in the untranslated 3' region. In these cases there may be multiple stop codons converted to selenocysteine. So, it is clear that SECIS is interacting with a ribosomal component and DNA base pairings.

coenocytic

Referring to a multinucleated condition resulting from the repeated division of nuclei without cytoplasmic division.

D loop

Region of mitochondrial DNA that contains an origin of replication and promoters; it is displaced during the initiation of replication, leading to the name displacement, or D, loop. Codes for rRNA, 13 subunits of enzymes that are essential for mitochondrial function.

puffs

Regions of active transcription. When the juvenile hormone ecdysone is added, a specific band always puffs first, then it recedes as others become activated in a cascade of developmental effects.

DNA topoisomerase

Relives additional coiling ahead of replication fork by breaking one strand and whip around to the other side

Exchange of plastids and genome rearrangement between Oenothera strains.

Repression of homologous recombination in a complete permanent translocation heterozygote and somatic segregation leading to sorting out of the two plastid types in F1 (I and II) allow the exchange of plastomes as well as haploid genomes (A, B, and C) in F2.

antibiotic resistance

Resistance evolving rapidly in many species of prokaryotes due to overuse of antibiotics, especially in agriculture.

Guevedoces

Results when a gene for an aromatase needed to complete male development isn't activated until puberty. At that time, what were ambiguous genitalia complete development into functional male structures.

RB gene

Retinoblastoma if both copies are missing, retinoblastoma is likely to occur. Gene expressed in many cells.

reduced penetrance example

Retinoblastoma, often first detected as a white or cherry red pupil in infants was long considered to be inherited as a dominant with reduced penetrance, since some individuals with the defective allele did not develop eye tumors. (Most cases had one eye affected but others had both.)

Retroviruses and retrotransposons

Retroviruses are RNA viruses that encode a reverse transcriptase used to make a DNA copy of themselves. The DNA can be inserted into the DNA of a host cell. They have long terminal repeats (LTRs) at each end that may act as promoters for adjacent genes. In some species, especially birds and rodents, the retrovirus sometimes excises carrying a neighboring oncogene; in that case transfer can lead to cancer. Rous sarcoma virus (RSV) is an example. The AIDs virus is a human example. It does not carry oncogenes but destroys T cells involved in immune surveillance for abnormal cells, thus leading to a high frequency of Karposi's sarcoma.

Rho-dependent termination

Rho (for release factor) recognizes a sequence (AAAAAAAU) and binds to the nascent mRNA, rapidly advancing to a stalled polymerase leading to release

indel

Runs of one base, ie AAAAAAAAAA

Prokaryotic Initiation of Translation

SD sequence is complementary to an exposed RNA sequence of the small 30s subunit of the ribosome. With the help the initiation factor, IF1, the mRNA is loaded onto the small subunit such that the AUG start codon in on the P-position of the ribosome. Then in the presence of IF3, a charged initiator tRNA which is fMet with a tRNAi with the anticodon for AUG is added and then with IF2 with a GDP molecule, the large subunit can be attached to form a 70s initiation.

Who inherits Huntington's Disease

SINGLE GENE DOMINANT INHERITANCE Rare, so unlikely to see homozygous individuals

snRNPs (small nuclear ribonucleoproteins)

SNRPs function to bring the ends of introns together.

Methods of ROS elimination

SSuperoxide dismutase (SOD) Catalase REDOX reactions

Sanger sequencing

Sanger sequencing based on 4 reactions, each with a different dideoxynucleotide. If incorporated, the didexoynucleotide prevents addition of another nucleotide to the growing chain., generating sequences of various lengths that encompass the entire original sequence. Terminated fragments are electrophoresed and the original sequence can be deduced.

Who is credited for cell theory and what year was it discovered?

Schleiden and Schwann in 1838-39

Three types of petites

Segregational Neutral Suppressive

Kuru

Similar to mad cow disease. At early ages, children would develop symptoms. Caused by infectious protein transferred by eating brain of deceased relatives.

Mendel Dominant and Recessive nomenclature

Since he started with true breeding parents, for example tall and dwarf, he concluded that each plant contributed one 'factor' to the progeny and introduced the concept of using capital letters for the dominant and the same small letter for the recessive factor (now allele). Although he wrote the genotype with the letters above and below each other, it is simpler to list the "monohybrid" (one gene) crosses as for example : TT (tall) female X tt (dwarf) male gave all Tt (tall) F1 progeny

ID vs Fraternal Twins

Since identical twins have the very same genes while fraternal twins only share some of the same allelic combinations, concordance (both twins the same) should be higher if the trait is genetic. If there is any environmental effect, there will be some level of discordance in identical twins. Remember that even with Aa X Aa parents, the probability that DZ twins will have the same genotype (both AA, or both Aa or both aa is) 6/16, so concordance for single gene traits will be fairly common. If multiple genes are involved, chance concordance in DZ twins drops rapidly, but not in MZ twins.

Now, how would you ever be able to identify where the cutoff for extreme phenotypes or the number of phenotypic classes in an F2 or other segregating population?

Since that is not possible, a different approach is needed that does not worry so much about how many genes or what each contributes is taken.

Gene-Centromere mapping

Since the centromeres always segregate in the first division of meiosis, the distance between a gene and its centromere can be calculated (ignoring mapping functions) as: ½ X the frequency of second division segregation

For I-1

Since two normal parents have a homozygous recessive affected child, the trait must be recessive and each parent must be heterozygous. P(het) =1

What do point mutations cause?

Single Nucleotide Polymorphisms (SNPs)

incomplete dominance

Situation in which one allele is not completely dominant over another allele

What are SRPs composed of?

Small cytoplasmic non-coding RNA and proteins

Okazaki fragments

Small fragments of DNA produced on the lagging strand during DNA replication, joined later by DNA ligase to form a complete strand.

phytoalexins examples

Solanaceae - sesquiterpenoids Leguminosae - isoflavanoids Malvacea - terpenoids

exception to one gene-one enzyme hypothesis

Some genes encode proteins that are not enzymes. Some genes encode a subunit of a protein, not a whole protein. Some genes don't encode polypeptides. Many genes function without coding a protein (ncRNA)

DNA telomerase

Special polymerase that can extend the lagging strand. Once DNA telomerase binds to the lagging strand, the RNA will extend past the end of the lagging strand and will serve as a template. DNA telomerase itself will then add bases to the end of the lagging strand that are complementary to the RNA that is found within itself.

Antibodies

Specialized proteins that aid in destroying infectious agents recognize foreign antigens

Chemical oligonucleotide synthesis process

Specific nucleotide sequences can be made, 1 step at a time. After each 'blocked' nucleotide is added, excess is washed out, the block removed and the next added

holandric examples

Sry, H-Y antigen and several genes involved in spermatogenesis

What does a polypeptide start and end with?

Start with amino terminal and end with carboxy terminal.

How Avery, MacLeod and McCarty demonstrated that Griffith's transforming principle is DNA

Started by purifying the killed smooth bacteria cells by separating its molecular components. Put each of the purified components on separate plates with live rough bacteria to see which plate would result in the rough bacteria gaining a polysaccharide shell. The only plate that did this was the one with DNA.

Hormones altering gene expression

Steroid hormones like testosterone, estrogen etc. can pass through the cell membrane, but join with a receptor in the cytoplasm to enter the nucleus and alter (up or down) transcription of target genes. In plants, the receptor elements for ABA are present in up to 7 copies/promoter. Copy number and slight changes in the elements can also affect the level of induced expression of ABA responsive genes.

Types of T cells

Suppressor Helper Cytotoxic

Transcription Activator-like Effector Nucleases (TALENS)

TALs discovered as 'effector proteins' secreted by Xanthomonas bacteria that cause diseases in hundreds of plant species; they are often products of Avr (avirulence) genes • TALs are secreted through a 'needle like' type III secretion system into host cytoplasm • If 'recognized' by a plant R gene (NB-LRR type) the host will trigger active host defense (= basis for the Avr designation) - host defense genes encode antifungal enzymes, phytoelexins, etc. • Each TAL can recognize specific host promoters and activate transcription of genes that enable disease to progress • Their structure revealed the basis for target specificity

knockout mouse experiment

Take a lambda clone containing portion of mouse CFTR gene and add selective marker (neo) and TK gene to CFTR restriction fragments. Then blastocysts from two agouti parents were placed on ES cell culture along with the previously constructed knockout DNA from mouse. Neomycin was then added to the plate so that only the cells containing the CFTR survived. Then two different things could happen. A double crossover could happen where a gene lacking TK is produced resulting in a knockout gene, or random integration could occur where the TK gene stays intact. The cells containing TK would die when gancilclover was introduced to the plate, resulting in only the double crossover cells to be present. Then a colony was formed with these cells. Ten of these cells were then placed in a mouse embryo. When the mouse develops, some cells will have knockout version of gene and some will not. Chimera will occur in those with the knockout gene.

Lysine ubiquitination

Targets wrongly folded proteins and signals for the destruction of the protein.

mRNA quantification using real time PCR after reverse transcription (qPCR)

Tells how many cycles it takes to detect a product

When does TT occur in linked genes

Tetratypes can occur from a single XO or 3-strand doubles, which can be distinguished if in a linear ascus.

What's special about 5.8S rRNA

The 5.8s is on a totally separate chromosome in humans and are transcribed by DNA polymerase III

Ames test

The Ames test is a useful tool for identifying chemical mutagens

F2 pod from selfing the F1 of a round by wrinkled cross

The LEGEND for a simple (one gene) Mendelian trait for this case would be written: R_ round (the underline indicates either allele may be present) rr wrinkled

When does the Poisson distribution become normal?

The Poisson approaches a normal distribution as the occurrences become less rare

Right arm of tRNA

The TYC on the right arm occurs in the majority of tRNA is thought to help tRNA stabilize on ribosome

chromosomal sex determination grasshoppers

The XO system as in grasshoppers and many bugs: females have 2 X chromosomes and males only one.

XY system

The XY system in Drosophila and animals; males are heterogametic, females homogametic. The Y has very few genes and is much smaller than the X.

AHS1 study

The accumulation of Ash1p results from ASH1 mRNA that is sorted as a ribonucleoprotein particle (mRNP or locasome) to the distal tip of the bud where translation occurs. To study the mechanism regulating ASH1 mRNA translation, we isolated the ASH1 locasome and characterized the associated proteins by MALDI-TOF. One of these proteins was Puf6p, a new member of the PUF family of highly conserved RNA-binding proteins such as Pumilio in Drosophila, responsible for translational repression, usually to effect asymmetric expression. Puf6p-bound PUF consensus sequences in the 3′UTR of ASH1 mRNA and repressed the translation of ASH1 mRNA both in vivo and in vitro.

Why do proteins fold?

The chains of amino acids can do some folding of their own into structures based on hydrogen bonding between the amino acids.

teratogens examples

The child on the bottom has the mimic, in this case caused by exposure to thalidomide in utero. Thalidomide, like alcohol and measles AND ZIKA viruses

concerted evolution

The common evolution of a family of repeated genes, such that changes in one copy of the gene family are replicated in other copies of the gene family.

Meiosis vs. Mitosis

The critical event that differentiates meiosis from mitosis occurs in prophase of the first division M1, when the homologous chromosomes pair 'gene-for-gene' in an event referred to as synapsis. Prophase of M1 has been subdivided into 5 stages to better describe the events that occur. After the first division, the daughter cells have one full set of chromosomes, even though each still has two chromatids that separate in MII.

lampbrush chromosomes

The description applied to chromosomes in which sites of active gene transcription can be visualized.

Built in signals aiding in alternative splicing

The enhancer elements [(exonic splicing enhancers (ESEs) and intronic splicing enhancers (ISEs)] are recognized by activator proteins (the SR protein family), and the silencer elements [exonic splicing silencers (ESSs) and intronic splicing silencers (ISSs)] are bound by repressor proteins [the heterogeneous nuclear ribonucleoproteins (hnRNP) protein family]. These two protein families are engaged to promote or inhibit spliceosome assembly at weak splice sites, respectively.

Reason that most eukaryotes have sexes

The fact that sexual reproduction allows new genotypes to occur and thus permits evolution by selection is assumed to be the reason most eukaryotes have sexes.

G1 phase

The first gap, or growth phase, of the cell cycle, consisting of the portion of interphase before DNA synthesis begins.

quarternary structure

The fourth level of protein structure; the shape resulting from the association of two or more polypeptide subunits.

Karyotype uncertainty

The groupings A-G indicated the uncertainty of being able to identify the specific chromosomes in a pair.

TOPO Cloning Vectors for PCR products

The kit includes a version of the topoisomerase enzyme that usually relieves supercoiling to ligate the insert into the vector at the TA/AT overlaps.

An EM view of the synatonemal complex with an interpretive drawing.

The lateral elements are zipped together by a protein called 'zip-1'

Euchromatin

The less condensed form of eukaryotic chromatin that is available for transcription.

suppressive petites

The mitochondrial defect is often a very large substitution of AT rich regions in the mtDNA which multiply much faster than the normal mtDNA so they basically take over 'suppressing' the other, after a few generations all will be petite.

Measuring h2 by results of selection

The most direct way to estimate h2 is to do an experiment and see what happens. The selection differential S is defined as the difference between the average value for the selected parents from the average of the overall population. When used as parents, the average in the next generation will typically show some regression toward the overall population average. The difference is called the Realized gain or R. h^2 is then R/S. If selection continued, h2 would change each generation as fewer segregating genes would be available

Rarity of generalized transduction

The odds of a specific gene being transferred and incorporated is only about 2 per million recipient cells.

Why the precursors in histidine synthesis were hard to find

The original compounds were phosphorylated and phosphotase was knocking the phosphate off. The reaction would not progress without the phosphate.

Meiosis as seen in spermatogenesis in animals diagram details

The pairing and random separation of homologous chromosomes to opposite poles explains why alleles segregate. The fact that crossovers occur provides the basis for mapping genes on the same chromosome: the farther apart they are, the more likely a crossover will occur between them.

Ultraviolet light mutations in exposed cells

The primary effect is creation of dimers between adjacent thymines 'stacked' in the same strand. On replication, the ability to pair with A is lost and if not repaired, a non-A nucleotide may be included in the new strand.

signal transduction pathway

The process by which a signal on a cell's surface is converted into a specific cellular response.

Reannealing

The process seen on cooling, where two complementary strands of DNA hybridize back into a single strand.

Termination of translation in eukaryotes

The same as bacteria, except all stop codons are recognized by one eukaryotic release factor (ERF)

Meiosis II

The second division separates sister chromatids to opposite poles.

G2 phase

The second growth phase of the cell cycle, consisting of the portion of interphase after DNA synthesis occurs.

secondary structure

The second level of protein structure; the regular local patterns of coils or folds of a polypeptide chain.

Primary structure

The sequence of amino acids in a protein structure is considered to be its primary structure. This would be a list of each amino acid used held by peptide bonds.

Pachynema

The stage in prophase I of meiosis during which the homologous pairs of chromosomes undergo crossing-over

Homozygosity

The state of possessing two identical forms of a particular gene, one inherited from each parent.

S phase

The synthesis phase of the cell cycle; the portion of interphase during which DNA is replicated.

tertiary structure

The third level of protein structure; the overall, three-dimensional shape of a polypeptide due to interactions of the R groups of the amino acids making up the chain. Can consists of alpha and beta proteins together.

For II-2 continued

The trait must be recessive; but since we know daughter II - 1 has the dominant phenotype, the probability she is heterozygous (i.e. Aa) is 2/3.

A polled bull from a cross between a PP polled cow and Pp polled bull could be either PP (1/2 chance) or Pp (1/2 chance). The first 5 calves when he is mated to pp (horned) cows are polled. Given this information, what are the odds he is Pp?

The two Hi's are that he is PP or Pp, and the Event is the 5 polled calves.

eukaryotic initiation of translation

There is no SD sequence in eukaryotes. Instead there is an eIF4F complex that has a cap binding protein (CBP) that recognizes the 5' cap of the mRNA and binds it, along with a eukaryotic initiation factor (EIF) that recognizes the poly-A tail and binds it and activates the mRNA. Once all of this comes together, it can attach to the small 40s subunit of the ribosome with a GTP and transcription factors attached. Now translation can start.

What does 70s mean?

These are not weights, it is how fast something will spin down in a particular kind of sucrose gradient. Not additive

Problems with these nonsense tRNA suppressors

They code for the same amino acid, so the finished protein still may not be correct. But, it could restore partial functionality.

Secreted proteins via translation through Endoplasmic Reticulum (ER) Outer Membrane

They have a signal sequence that starts the translation on the free ribosome. When the signal is finished, it interacts with a signal receptor particle (SRP) and that then binds the ribosome to the rough endoplasmic reticulum. Then the rest of the protein is excreted into the lumen of the ER where many kinds of changes can occur to the protein before it is transported to the desired destination.

How antibiotics work

They prevent the binding of tRNA for certain amino acids on to the binding site of the ribosome.

Epistasis in biosynthetic pathway

This is often a case where both genes are in the same biosynthetic pathway. Since two genes are involved, the clue is a modified F2 dihybrid ratio i.e., rather than 9:3:3:1 the ratio may be 15:1, 9:3:4, 9:7 13:3, etc. Here either cc or pp masks expression of a dominant at the other locus.

Microdeletions in DiGeorge Syndrome

This shows some deletions that 'uncover' genes that are assumed to be responsible for the phenotype In the study this figure came from, FISH and quantitative Multiplex Ligation Probe Amplification with 30 probes in the region were used to identify regions where only one copy of the gene is present. As should be expected, there is a lot of variability in the phenotypes of affected individuals, which involves neuropsychiatric (mostly ADHD) and head/facial abnormalities.

Mouse Lymphoma Assay

This system allows detection of mutations that lead to loss of function of a specific mouse gene; Positive selection (cells grow in a special medium only if the only copy becomes defective)

amplified fragment length polymorphism

This technique is useful for detecting diversity among samples. By adding adapters to each end of restriction fragments, the same primers can be used to create gel patterns. If one primer is labeled with a fluorescent dye, automated detection is possible.

Microarrays

Thousands of nucleic acid sequences are arranged in grids on glass or silicon. DNA or RNA probes are hybridized to the chip, and a scanner detects the relative amts of complementary binding. Used to profile gene expression levels or to detect single nucleotide polymorphisms (SNPs). allow mRNA levels of many genes to be measured all at once

Structural - induced

Tissue level Cellular level

Why are some bases methylated?

To differentiate the old strand with the new strand in DNA for repairs.

Transcripts in mitochondria

Transcripts in mitochondria are separated by endonucleases that clip out tRNAs. Specific endonucleases clip the 3' and 5' end. Then a CCA is tacked on. Enzymes that achieve this are produced in the nucleus.

Robertsonian translocation

Translocation in which the long arms of two acrocentric chromosomes become joined to a common centromere, resulting in a chromosome with two long arms and usually another chromosome with two short arms. Chromosome number 2 in the previous flashcard

Problems of Barbra's experiment

Transposons were not easy to describe. This made her papers difficult to read.

What happens when peptide hormones interact with membrane receptors?

Triggers a cascade of events referred to as a signal transduction pathway, often starting with a tripartite "G protein" to create a second messenger

Triploid glass carp

Triploid grass carp have been created by temperature manipulation of oocytes before fertilization to create sterile 3N fish to help get rid of plant and algae overgrowth without risk of reproducing which was spoiling sport fishing in lakes such as Lake Conroe.

Presumed origin of modern wheats

Triticales is a man made species created from a cross of hexaploid wheat to rye (N=7, its R genome also has 7 chromosomes) in order to introduce a gene for disease resistance. It is AA, BB, DD, RR.

2019 human use

Two companies reported using ex-vivo bone stem marrow cells to 'cure': b-thalassemia Lack of b-globin, often due to a deletion or altered promoter Sickle cell anemia SNP that causes a missense in b-globin Both patients could stop having frequent transfusions, so far 9 month and 4 months, respectively.

If the third base of an anticodon is a A, it can pair with...

U

UBE3A

UBE3A on chromosome 15 is silenced in male gametogenesis or spermatogenesis and not expressed in the zygote; if the female version of the gene does not function, the child will exhibit Prader-Willi syndrome (mental retardation and obesity)

Transcriptional activation of Gal4

Under non‐inducing conditions, Gal4 activity is blocked by the interaction of Gal80 with the Gal4‐activation domain. Gal4 levels are regulated by the F‐box protein Grr1. On galactose induction, Gal80 is removed from the Gal4‐activation domain, which is then able to recruit the transcriptional machinery. Dsg1 regulates turnover of transcriptionally active Gal4. GTFs, general transcription factors; SAGA, Spt‐Ada‐Gcn5 acetyltransferase; TBP, TATA‐binding protein. Gal3 is thought to convert Galactose to an actual inducer and then seems to hold Gal80/inducer in the cytoplasm. Gal3 is not made if glucose is present.

Illumina sequencing

Used to generate hundreds or thousands of short reads that can be assembled based on overlapping bases.

golden gate cloning

Uses type 2s restriction endonucleases such as BsaI that recognize one site but cut beside it; can assemble a series of components into the same plasmid for expression.

Intraspecific animals

Very few interspecific crosses are successful in animals and if it does occur the interspecific progeny are typically infertile. A well known example comes from crosses between horses and donkey, both in the genus Equus but different species. The progeny of a male donkey and female horse is a mule, which has 63 chromosomes per cell: 32 from the horse and 31 from the donkey. In a few documented cases a female mule has had an offspring, but no male mules have been demonstrated to be fertile. The reciprocal cross, which seldom occurs produces a Hinny in which both sexes are sterile.

The discovery of a trait that shows maternal inheritance

Was looking at the inheritance of the collar of plants, and he found the first case of non-mendelian inheritance. He had plants that were white, green, and variegated. He found that wherever the female came from it doesn't matter where the pollen comes from, the progeny is always the same color.

Triploid Plants: 4N X 2N --> 3N

Watermelons: the tetraploid by diploid cross has to be recreated every generation, so its useful to use markers to tell which progeny are hybrids, which produce no seeds Bananas: Most commercial bananas are triploid and seedless.

Why the frequency of 2nd division segregation is never greater than 2/3

We are 'sampling without replacement': if a centromere with an A mating type allele happens to go to the pole first and segregation is random, there is a 2/3 chance the next spore will have an a mating type allele.Thus the maximum f(2nd division segregation) is 2/3

glucose enzyme

What happens is that there is a place on the surface of the enzyme that is referred to as the active site. In this case the active site is a perfect fit for ATP and glucose. Once the ATP and glucose are connected to the enzyme, then a phosphate will be transferred to a glucose, making glucose-6-phosphate and ATP is reduced to ADP. In this case, the enzyme would not be reversible, but the enzyme if available when this same reaction is needed.

Cot curves of eukaryotic DNA reveal differences in the copy number of some fragments

When DNA is chopped up, melted, and allowed to reanneal, highly repeated sequences can rapidly find a partner, others take a bit longer and finally unique sequences find their partner over varied periods of time, as seen with these 'bumpy' curves typical of organism with large DNA content.

Ef (elongation factor) - Tu - Ts cycle

When EF-Tu is charged with a GTP and bound to tRNA that is charged it allows the tRNA to enter the ribosome onto the A site. The EF is then released from the tRNA, now with just a GDP. Now, elongation factor Ts can replace the GDP. Then the Ts can be replaced by GTP and the process restarts.

Excision repair in E. coli

When a double-stranded DNA molecule contains a lesion, the enzyme uvrABC endonuclease nicks the DNA strand on both side of the lesion. DNA polymerase III then uses 3' to 5' nick translation where it takes out all bases within the nicks. Then it uses the correct bases to fill in from 5' to 3'. Ligase then seals the nicks.

Bottleneck

When a large population is reduced to a few surviving individuals

DNA repair in E. coli

When a mismatched pair is found, enzymes called MutH and MutS creating nicks on both sides of the mismatched pair, on the new strand. Then DNA polymerase goes from 5' to 3' to correct the mismatch.

MAX Bac

When baculovirus bacteria sequence was inserted in cell by transformation, then the protein that was coded would come out like those of mammalian systems.

How to make coding sequences easier to read

When different fluorescent dyes could be incorporated into each of the the ddNTPS, separation of the products by size with a detector made it possible to directly 'read' the last base added based on size. These could also be placed directly into a computer file, which greatly reduced transcribing errors and simplified comparisons to other sequences.

cAMP and CAP regulated Operon

When energy begins to become limiting, a signal molecule (cAMP = cyclic-AMP) builds up, binds to a catobolite activating protein (CAP); and the complex in turn binds to a site between the promoter segments of the lac operon. Binding of the cAMP/CAP complex opens the promoter for RNA polymerase binding

Using Heritability

When genes contribute to variation in useful or desired traits, selective breeding allows 'gains' to be made.

Recessive lethal balanced by mutation

When homozygous recessives cannot reproduce, the q value will become very small. In the meantime, new A to a mutations will 'replenish' q.

Epistasis

When one gene or genotype masks expression of another

Species specificity of Internal Transcribed Spacers

While the tandem copies of rRNA must be highly conserved to function in ribosomes, the same is not true for the spacers. So long as the borders used for excision remain, the other bases can change. This has led to the situation where ITS 1 and ITS 2 remain the same within a species where crosses occur via concerted evolution, but they tend to differ between species. Because the flanking rDNA components are so highly conserved, it is easy to use PCR to amplify one or both and then compare sequences.

Three kingdoms

Woese used ribosomal DNA sequences to show that archeobacter are as different from eubacteria as are eukaryotes, giving rise to the three kingdoms of life concept.

Wolbachia gene drive

Wolbachia bacterial infection tends to alter sex ratio so has been suggested for some time to be a potential gene-drive organism versus malaria. Now CRISPR-based homing gene drives minimally include Cas9 endonuclease, which facilitates the genome integration of the gene drive and a guide RNA (gRNA) cassette, which encodes the sequence-specific integration site targeted by Cas9. When these two components are expressed together in the germline at the correct time and quantity, they can cause drive by inducing gene conversion to replace a normal gene with one including the Cas9 transgene so both copies are defective

Barbara McClintock- about 1963M MUST REMEMBER NAME FOR DEGREE

Won Nobel prize where she described pairs of genes in maize that would jump around in the genome and cause disruption at other loci. There turned out to be elements that code for a transposase that allows other components to move to a new location of the chromosome.

Albert Kossel (1890-1910)

Won nobel prize in 1910 for proving that nuclein contained four different bases, along with the differences between purines and pyrimidines. Also credited for discovering the amino acid histidine.

Yanofksy's work with TryA mutants

Worked with TryA gene. He found mutations a site A446 where a tyrosine was supposed to be. He also a mutation at site A46 where glycine was supposed to be. If you had a A46 mutant that was glutamic acid, the protein was non-functional. If you had the A446 mutant with cystine, the protein was non-functional. However, if both the A446 and A46 site had the mutation, then the protein was functional. This revealed that one of these mutations is a suppressor of the other.

Ames' work with neurospora

Worked with mutants that blocked histidine production. So he isolated a series of different auxotrophs. He knew that they were each single genes and they were different genes. He then tried to see what would crossfeed what or what would block and accumulate in particulate mutants. His first problem is that nothing accumulated if it was grown in histidine, because of gene regulation (if you give them histidine, they stop making it). If you provided very little histidine, then each mutant, except C94 which grew no precursors, accumulated X, Y, and Z. To figure out the pathway to histidine production, he used double mutants. In double mutant with C94 grew no precursors. Double mutants with C-84 grew X. Double mutants with C141 grew Y, and double mutants with T1710 accumulated Z. When the pathway was put together, you understand why each would accumulate.

Friderich Meicher (1869)

Working with cells that came from hospital bandages, i.e. puss. After treating the puss with HCl for a few weeks, the cytoplasm would dissipate and only the nuclei remained. Found that the nuclein contained lots of phosphorus.

Beadle and Tatum use of Neurospora crassa

X-rays were only known mutagen at the time, so Beadle and Tatum exposes Neurospora to it. They were also concerned that the average conidia spore had more than one copy of the nucleus. They irradiated conidia and then used them as a male in a cross. Then, they selected one spore out of each ascus to go on, which means they were losing half of their potential mutants. They were then allowed to grow on complete medium and then on minimal medium. If it couldn't grow on the minimal medium, then there was a mutant that was preventing the growth. They moved the non-growing sample and moved it to a minimal medium with all amino acids. If it grew here, then they placed the sample on different mediums with each individual amino acid. The ones without growth indicate that this amino acid is required for growth.

Turner's female

XO: short stature; webbing of the neck; may have low mental ability and sterility.

Global changes in yeast cells

Yeast cells starved for an amino acid add a phosphate to eIF2, which prevents transcription from almost all promoters, but stimulates a few to become more active.

Cytoplasmic inheritance in yeast

Yeast of opposite mating types fuse to form a diploid before in mating, so there is a mixing of cytoplasm. However, cytoplasmic inheritance can still be observed. Yeast can grow by fermentation without functional mitochondria, but in doing so forms relatively tiny 'petite' colonies. This reflects the fact that glycolysis provides only 2 ATPs per glucose rather than 30 from oxidative phosphorylation using mitochondria. There are 3 types of petites as will be described.

Fragile X Syndrome

a disorder produced by injury to a gene on the X chromosome, producing mild to moderate mental retardation caused by expansion of non-coding trinucleotide repeats

Human Karyotype

a display of the full set of 46 human chromosomes

lac operon

a gene system whose operator gene and three structural genes control lactose metabolism in E. coli

CFTR gene

a gene that codes for a protein involved in chloride and water transport across membranes. In patients with cystic fibrosis, a mutation in this gene disrupts chloride and water transport across membranes. The end result is production of thick and sticky mucus that obstructs the airways in the lungs and the ducts in the pancreas.

knockout mouse

a genetically engineered mouse in which the code for a particular gene has been disrupted

Sweet Genes

a large gene family that is highly conserved that can allow sugars like sucrose to be exported outside the cell and thus available to the bacteria

Centrioles

a minute cylindrical organelle near the nucleus in animal cells, occurring in pairs and involved in the development of spindle fibers in cell division.

DNA probe

a molecule labeled with a radioactive isotope, dye, or enzyme that is used to locate a particular sequence or gene on a DNA molecule

auxotroph

a mutant organism (especially a bacterium or fungus) that requires a particular additional nutrient which the normal strain does not.

genomic imprinting

a phenomenon in which expression of an allele in offspring depends on whether the allele is inherited from the male or female parent

Cistron

a section of a DNA or RNA molecule that codes for a specific polypeptide in protein synthesis

primer

a short stretch of RNA with a free 3' end, bound by complementary base pairing to the template strand and elongated with DNA nucleotides during DNA replication

corepressor

a small molecule that cooperates with a repressor protein to switch an operon off

Treatment for PKU

a special diet, low in phe (Lofenalac, for example), at least until brain development is advanced. The recommend diet is mostly fruits and vegetables

aberration

a state or condition markedly different from the norm

goodness of fit test

a test for comparing observed frequencies with theoretically predicted frequencies

p53 protein

a tumor suppressor gene that is critical for signaling that DNA repair is completed before cell division continues. Alternatively, if there is too much damage it triggers apoptosis, or natural cell death.

CRISPR/Cas9

a unique technology that enables geneticists and medical researchers to edit parts of the genome by removing, adding or altering sections of the DNA sequence

Environmental effects on mRNA stability

a-amylase in germinating barley aleurone has 100 h half life reduced to 30 min if heat shock

gene regulation

ability of an organism to control which genes are transcribed in response to the environment

Frequency of PD and NPD

about the same

hydroxyprolated glycine in COLA1 and 2

accounts for flexibility of fiber

Histone acetylation/deacetylation

acetylation removes positive charge and allows DNA to be opened because phosphate of DNA is positively charged

Role of snoRNP

act as guides to change specific U's to pseudouridine (𝛙) and to methylate riboses

Kinases

activate another protein by adding a phosphate which is often passed to the next member of the chain

TdT (transferase)

adds tails of available base

Mutagen

agents that cause mutations to occur

Teratogens

agents that causes birth defects, not by mutation, but by inhibiting development

universal

all organisms use the same code (with a few exceptions in special situations)

amphidiploid

allopolyploid consisting of two combined diploid genomes When similar species can cross-hybridize, subsequent spontaneous or induced chromosome doubling creates a fertile plant that is 'amphidiploid'. Brassica species are a classic example even when the parents have different numbers of chromosomes.

TYC arm on tRNA

allows H-bonding to the large rRNA subunit

yeast 2-hybrid system

allows for the identification of proteins that directly interact makes use of two fusion proteins and a reporter You make a library of from one gene acting as 'bait', and then in another library you put a whole bunch of other proteins that could potentially interact with the bait protein. Then you could use a dye to see which proteins interact with each other.

types of secondary structure

alpha helix and beta pleated sheet

Zinc finger proteins

also trans-acting factors that can recognize and interact with specific response elements in a promoter.

Alternate splicing drosophila

alternate splicing leads to sex of Drosophila Note males include exon 3 of Sxl which has a stop codon. If males express Tra, the mRNA is not spliced and has a stop in what would be the the first intron. This leads to different forms of the DSX protein, also via altertive splicing with male and female determining sex. (G. Saccone photo)

Where does miRNA processing occur in plants

always in the nucleus

What are amino acids composed of?

amino group on one end and carboxyl group on the other

How dsRNA is amplified in a plant

an RNA-dependent RNA polymerase (RdRp) can amplify short dsRNAs that can then spread through the plant

disomic

an abnormal haploid carrying two copies of one chromosome

conditional lethal

an allele that is lethal only under certain conditions

nonparental ditype (NPD)

an ascus that contains cells that all have a nonparental combination of alleles.

parental ditype (PD)

an ascus that contains four spores with the parental combinations of alleles

intrinsic transcription termination

an inverted self complimentary DNA sequence can cause stem-loop hairpins to form in the DNA followed by a run of around 7 As. When the polymerase stalls going through the hairpin, the U:A region unravels and allows the mRNA to be released

Holoenzyme

apoenzyme + cofactor

constituitive genes

are constantly expressed

kinetochores

are the proteins (>/= 19) attached to the centromeres and to which the spindle fibers attach

How much bacteria undergoes transformation?

around 1%

Rate of transcription in prokaryotes

around 1000 bases per minute

Genome size of E. coli

around 5 million base pairs

When can prokaryotic translation begin?

as soon as the leader portion of mRNA is available after transcription

When are dominant mutations seen?

as soon as they happen

How many different alleles of gene can diploid individuals have?

at most 2 However, there can be many different mutations in the same gene when considered on a population basis

gRNA

"guide" RNA that adds or subtracts U's from mRNA i.e. in protozoan mitochondria

Trisomy

(2N+1) -generally detrimental also, but some can survive •In humans trisomy 21 (47 XX or XY +21) is the most common -this formerly was referred to as Down's syndrome, for the man wo described it -risk increases with the age of the mother »the risk of nondisjunction of the paired # 21 chromosomes that were paired and started meiosis early in embryology of the female increases over time there is a slight increase with the age of the father

Trisomy 13

*Extra 13th* chromosome 47 instead of 46 chromosomes Severe birth defects: clefts, extra fingers/toes Often heart, brain or spinal abnormalities Short life span Patau's syndrome

population genetics terminology

, 'gene' frequency is used instead of allele frequency, and the f(dominant allele) = p while the f(recessive) = q Thus with 2 alleles p + q = 1

N-terminal amino acid affecting half life of proteins

- <3 min in yeast if the N terminal amino acid is arg, lys, phe, leu, or trp - >20 hours if it is cys, ala, ser, thr, gly, val, pro, met

Drug resistance in bacteria

- Staphylococcus samples from pre-1940 have no antibiotic resistance genes. 1947: 38% had, 1969: 69% had and now essentially 100% carry genes for antibiotic resistance

Disease resistance genes in crops often have a short useful life before mutation/recombination overcomes the barrier

- gene for gene evolution concept: R in host versus virulence in pathogen - R genes often 'recognize' a pathogen component and trigger a defense response; loss or a change in the pathogen component leads to renewed virulence - multigene resistance is often more durable, even if less than full resistance is present

Bacteria often contain R (resistance) plasmids with multiple resistance genes

- some plasmids can transfer to multiple species (promiscuous) - resistance genes in a host can enter the plasmid via transposons - hospital samples average 3 different R plasmids/cell, most with resistance to >1 antibiotic - a 1998 case where multiple individuals taking antibiotics were sickened (some died) had Salmonella newport from 'tainted' meat with a plasmid providing chloramphenicol, streptomycin, sulfa-methoxazole, tetracycline, amoxicillin, ampicillin, cofixtin, ceftiofur, and cephalothin. The antibiotic eing taken gave the resistant strains a huge advantage over the normal resident bacteria.

Other mechanisms for creating deletions include:

-'unequal crossing over' due to false alignment of homologues - crossing over between inverted repeats as may occur when transposons are present -errors in DNA replication, especially in repeat areas -segregation from inversions and translocations that will be discussed later

LINEs (long interspersed nuclear elements)

-100,00 or so copies of L1 in humans -6-7 Kb; rarely expressed reverse transcriptase -Likely origin is a retrotranspon -SINES (alu is an example) < 700 bp, often tRNA in center

•Each gene shows incomplete dominance:

-A'A' contributes 2X as much as A'A, etc, -A', B', C' etc are 'contributing alleles'. -A, B,C etc., or a, b c, are non-contributing as far as the defined phenotype is concerned.

•If genes A and B are on different chromosomes, we expect to see the meiotic products of an AB X ab cross to come out, by chance as

-AB, AB, ab ab (parental ditype or PD ascus) -Ab, Ab, aB, aB (nonparental ditype or NPD ascus) -and if there is a crossover between one of the genes and its centromere (or both in some cases) we should see an AB, Ab, aB, ab (tetratype or TT ascus)

Yeast Budding • after mitosis, ASH1 mRNA localizes in the region of the daughter nucleus • under starvation conditions, yeast can switch to a filamentous type of growth

-ASH1 protein prevents any mating type switching -a hairpin in the 3' UTR of the mRNA is recognized by protein She2 that links ASH1 mRNA to a motor protein that propels mRNA in granules along the polarized actin fiber tubules • Puf6 binding prevents connections to the 5' CAP binding complex which is required for translation •mRNAs in RNP-bodies (granules) often also have the polyA tail clipped off (it is later regenerated) *Puf6 protein represses translation of Ash1 mRNA before it is in the bud.

examples of dominant lethals

-Achondroplastic dwarfism in humans -Tailless in mice -creeper chickens - White color in horses --Powder puff dogs In each case, affected by affected gives 2/3 affected, 1/3 normal

Terminal deoxynucleotidyl transferase (TdT)

-Add tails to 3' ends A's to one fragment, T's to another for example -Creates sticky ends

Angelman Syndrome

-Angelman syndrome reflects a missing or inactive adjacent region of Ch 15 that should be active in female gametes

Identifying clones by sequence homology

-Base sequences in GenBank -Translated into proteins of known amino acid sequence -DNA hybridization

Binding of ubiquitin to proteins

-Binding can target cyclins, transcription proteins etc., so can alter cell division, gene expression, etc. as well as causing protein turnover.

Where the binding of ubiquitin occurs

-Binding connects the C-terminal gly of ubiquitin to side chains of lysine, can be multiple sites -Binding will occur when misfolding exposes a binding site

blue-white screening

-Blue colonies do not have vector with foreign DNA inserted -White colonies have foreign DNA inserted

Identifying clones by expression

-Complementation; a functional gene replaces function in a mutant strain -Enzymatic activity where functional; often uses Pichia pastorus, a type of yeast that makes similar protein modifications as higher organisms -Baculovirus expression in cultured insect cells (MaxBac) from Max Summers, TAMU Entomology

Plasmids as a vector

-Developed from natural plasmids; circles of DNA that can replicate in other cells (mostly E. coli)

Chiasma interference

-Does a crossover alter the chance of a second nearby crossover? -In most cases, the answer is yes; that is, the coefficient of coincidence is reduced, especially if the distance is short -in Aspergillus nidulans, the answer is no -There are cases where 'negative interference' is detected, ie, there are more double XOs in a small region than predicted by chance

Chromatid interference: are the same chromatids involved in nearby crossovers more or less frequently than expected by chance?

-Double crossovers should occur in a 1 two strand : 2 three strand : 1 four strand -In N. crassa the ration of more like 5:8:3, meaning the same two strands are more likely to be involved than all four strands

So, how we respond to so many diverse foreign invaders can be explained by:

-Due to the millions of possible combinations of different H and L chains to make an antibody, along with the fact that the junctions are often sites of base insertions or deletions and the observation that 'hypermutation' is a feature of mature somatic B cells, it is estimated that humans have an antibody repertoire of at least 1011 . -Most antigens have multiple epitopes, so multiple antibodies are made -Monoclonal antibodies can be made using 'hybridoma' technology

We do not have millions of antibody genes, but can generate millions of different antibodies.

-Each B cell only makes one specific antibody which is initially on its cell surface; -An antibody is fairly specific so far as the antigen that it will recognize (the target on an antigen that the antibody 'recognizes' and binds is called an epitope) -The B cell engulfs the antigen, partially degrades it and presents fragments on the cell surface in its MHC (major histocompatibilty complex) surface proteins; -If a helper T-cell, via a T cell receptor surface-bound protein, recognizes the bound antigen, it 'activates' the B cell to make and pump out antibodies that target the invader for destruction, including digestion by macrophage cells. Activation involves chemokines and interleukin. Abnormal cells such as cancer cells are also recognized.

other trisomies in humans

-Edwards syndrome or trisomy 18 -Patau syndrome or trisomy 13 -Trisomy 22 can occur but is almost always aborted spontaneously in the first trimester and those born live less than a day

Gregor Mendel unique approach

-Examined individual characters with simple alternatives -Kept pedigrees for multiple generations -Kept track of numbers of each type of progeny

dosage compensation

-Homozygous females and normal males equally express X-linked genes -Heterozygous females may show variable levels of clotting factor and other X-gene products -Where expression can be seen on a single cell level (such as staining cells for G6PD expression) heterozygous females have a mix of both types

Phenotypes can also reflect a failure to properly imprint

-If IGF2 and H19 genes both show the typical male pattern of expression, the risk of cancer is greatly increased. -Beckwith-Weidemann disease causes abnormal growth if regions of Ch 11 are not properly imprinted.

Characteristics of Neurospora crassa

-It produces millions of identical spores (conidia) asexually -It grows as a haploid, so new mutants are not masked by a dominant allele -Controlled crosses could be made between strains of mating types 'A' and 'a -It could be grown on a defined 'minimal' medium, containing only essential elements (C, H, O, P, K, N, S, Ca, Fe, Mg, Cl, a few trace elements such as I, Mo, Mn, Se and Cu, etc) and one vitamin, biotin

protein activity modified by kinase

-Kinases add phosphates, Phosphatases remove them

Leucine rich repeat (LRR)

-LRR allows interaction with another protein (pathogen elicitor?)

Phage T4 polymerase

-Label DNA for use in hybridization, sequencing etc.

•Some traits that 'run in families' may not be inherited:

-Language -Religion -Pellagra (Vitamin B3 deficiency) -Kuru

•Many traits such as feeble minded or criminality assumed to be inherited in rather simple fashion

-Led to laws allowing forced sterilization; 60,000 cases in US by 1936 when the 'science' and methods agencies used to identify targets was finally banned •Supreme Court upheld sterilization of Carrie Buck in1927 -Taken further by Hitler; over 350,00 sterilizations even before the death camps •May contribute to the widely held concerns dealing with 'genetic engineering' as is possible today

Alternative splicing in insulin receptor in humans

-Liver; 20 exon form has low insulin affinity -Muscle; exon 11 (12 amino acids) omitted gives high affinity form

Guthrie test process

-Media prepared containing b-thienylalanine, a toxic analog of phenylalanine is impregnated on a card added to a plate with bacteria. -If a heel prick of blood from a newborn contains excess phe, when spotted on the card, a strain of B. subtilus will grow at that spot since analog uptake is out-competed by an excess phe; for normal blood spots, no colony is formed since the toxic analog is taken up. -Retesting is critical as some false readings occur. Nowadays Tandem Mass -Spectrometry can be used instead of the Guthrie test or for verification -

conditional lethal examples

-Mutations to alleles that are temperature sensitive, or that allow survival on one medium (food) but not another make it possible to study events and genes involved in development, formation of macro-molecular structures, etc. -Heterozygous advantage in sickle cell anemia will be considered later

Nucleotide binding site (NB)

-NB initiates a signal transduction pathway to activate defense genes •chitinase, glucanase etc to break down insect or fungal cell walls •ROS generation •Phytoalexin biosynthesis pathways (phytoalexins are host specific compounds with anti-pathogen or insect activity) -terpenoids -Phenylalanine ammonia lyase (PAL) pathway derivatives

What is the probability that 2 tasters from the population who marry will have a nontaster child?

-P (mom is heterozygous) X P ( dad is heterozygous ) X ¼ since only one in 4 children will be tt Thus, the answer is ¾ X ¾ X 1/4.

Prader-Willi Syndrome

-Prader-Willi syndrome arises if the male-active region of Ch 15 is defective •A snoRNA that is needed in the brain to correctly splice a serotonin receptor mRNA is not expressed

Huntington's disease symptoms

-Progressive loss of controlled movement -neurodegenerative disorder; loss of cognitive function -depression, aggression are often later symptoms -death 10-15 years post beginning of symptoms -'anticipation' earlier symptoms next generation

Useful properties of bacteria for genetic study

-Rapid growth; up to 109/ml overnight -Haploid, even if more than one copy of DNA per cell -Replica plating allows rapid screening of mutants and recombinants -Small genomes

'2-factor' systems

-RsmA can prevent translation, increase mRNA degradation if it is no longer bound by a noncoding RNA made by RsmB -GacA and GacS can alter RsmB expression and also allow expression of alternate sigma factors HRP-L, RPO-S RPO-N

•Heterozygotes, with duplicated normal and translocated chromosomes form a cross configuration in synapsis in order to pair 'gene-for-gene'

-Segregation of adjacent centromeres in heterozygotes to the same pole leads to semi-sterility (both sexes) -Translocations can contribute to speciation as a result of the reduced fertility of heterozygotes.

•SnoRNA-mediated modifications of rRNA

-Sno (small nucleolar) RNAs act as guides to: •Methylate 2' Os on specific riboses •Change some U's to pseudouridine

Deciphering allele origins

-Sometimes modern methods can help decipher the alleles and origin: A relatively high frequency of Tay-Sachs in maritime French Canadians and Louisiana (Cajuns) was assumed to reflect the expulsion of French sympathizers from Nova Scotia (Acadia) during the French and Indian war (1775-1763). However, the alleles in the Cajuns are the same as those in Ashkenazi Jews, another high risk group whereas the French Canadians have a deletion in the 5'- leader area.

Tay-Sachs

-Tay-Sachs infants do not survive beyond 3 years of age

founder effect examples

-The Amish in Pennsylvania have I in 400 frequency of maple-syrup-urine disease vs 1 in 250,000 in the general population; they also have more cases of polydactyly and 20 of the 35 known cases of Crigler-Najjar syndrome known in the US, a disease that can be treated by long exposure to blue light. -Creutzfeld Jacob disease (the human equivalent of 'mad cow' gene) inheritance in Italy, Tunisia, and Chile all trace back to a family from Spain. -Pitcairns Island was established by 8 men (6 mutineers from the Bounty) and 8 Tahitian women in 1790; one man seems to have left way more alleles than the others. -The "Dunkers" a religious sect that left Germany have no 'B' ABO alleles versus 10% overall

mechanism to equalize expression for genes on the X in XX and XY individuals in drosophila

-The SXL gene product which is present only in females blocks translation of the mRNA made by MSL-2 (males sex-lethal) -Removal of an intron and translation of MSL-2 mRNA thus only occurs in males -The MSL-2 protein binds to the one X chromosome present, recruits histone acetylase H4Ac16 which 'opens' the chromatin so that twice as much mRNA is made from the genes on that X.

examples of multiple alleles

-The coat color alleles are listed in the order of dominance

Key components of RNAi

-The enzyme dicer -Ago2 or other 'argonaute' proteins -The RISC (RNA Induced Silencing Complex)

PARs (pseudoautosomal regions)

-The tips of the Y have homology to sequences in the X. These PARs (pseudo autosomal regions) allow X-Y paring in meisosis I of a male. Genes in the PAR region do not show sex-associated patterns of inheritance -The Y also encodes some snRNAs

piRNAs (piwi-interacting RNAs)

-They are similar to argonautes, but lack one of the conserved sequences. Most piRNAs appear to derive from long single-stranded RNA precursors encoded by repetitive intergenic regions. The RNA interacts with PIWI proteins to guide germline development and gametogenesis of many metazoan species, from germline determination and germline stem cell maintenance to meiosis, spermiogenesis, and transposon silencing.

sex-limited traits

-Traits such as lactation that occur only in one sex although genes and alleles are present in both

sex-influenced traits

-Traits that are dominant in one sex, recessive in the other •Cannot be genes on the X or Z chromosomes

conidiation in fungi: tools •Neurospora and Aspergillus have been widely studied. •In addition to being haploid for almost all the life cycle which allows rapid discovery of aconidial mutants, the following tools are available:

-Transformation, generally after creating protoplasts via wall digesting enzymes, -Homologous recombination is common, allowing the creation of •gene knockouts, by transforming with a selectable marker flanked by segments of the target gene, •gene knock-ins, in which a candidate gene clone from the same or a different species is introduced: function is confirmed if complementation occurs -In mus (mutagen sensitive) mutants, non-homologous end joining, which leads to ectopic (random) integration is eliminated, so that homologous XO is ≈90%.

Vent polymerase

-Used for PCR, DNA amplification

Other roles of DNA methylation

-X chromosome inactivation in mammals -Genomic imprinting

Barr bodies are inactive X chromosomes

-XY Males have no Barr bodies, XX females and XXY males have 1, XXX females 2, etc.

•Charles Burnham spent a 50+ year career attempting to create a similar situation in maize

-a line with all chromosomes involved could be used to create doubled haploids from progeny of crosses -he did not succeed

Bottleneck examples

-a tree that survived a forest fire is heterozygous for what was a rare allele in the larger population. -Of the 20 survivors of a Typhoon that struck Pinjelap Island in the South Pacific in 1900, at least one had an allele for achromatopsia (total colorblindness); the frequency of that recessive allele in the current Pinjelap population is 0.25 but extremely low around the world. -the elephant seal population was reduced to about 20 individuals by hunting; todays much larger population still has limited genetic variability. -Florida panthers were reduced to six individuals; the current genetic diversity is about 1/3 that of museum specimens. Only one mitochondrial type remains. Crosses have been made to Texas panthers to try to maintain the gene pool and prevent extinction.

Proposed explanations for this concerted evolution include:

-cycles of unequal crossing over, -expansion/contraction might expand a particular form and eliminate another, -gene conversion from mis-paired alleles would favor most common form. •And yet: duplicated copies of the globin genes have evolved to be separate genes and provide alternate functions.

•What prevents total genome instability

-defective Ds elements can 'tie up' the transposase. -multiple repeats present in the genome lead to inactivation of expression via DNA methylation.

For aberration, consider:

-definition -genetic consequences if heterozygous or homozygous -chromosome pairing/segregation in heterozygotes and homozygotes -effects on gamete fertility -role in evolution

•Gene interactions are not critical in that there is/are no:

-dominance, -epistasis, -modifier genes, -cytoplasmic inheritance/interactions -maternal effects, etc.

Hfr conjugation

-donor HFr cell has F factor integrated into its chromosome -donor genes are transferred to recipient cell -a complete copy of the F factor is usually not transferred -gene transfer can be clockwise or counterclockwise

Duplications can arise by several mechanisms:

-error in DNA replication -reverse-transcription of a mRNA that is re-incorporated into the genome -crossovers in an inversion - especially in bacteria, transfer of a copy between a pair of insertion elements

X is often used as the basic number in amphidiploids

-example, wheat 2n = 6x (21 pairs with 7 chromosomes/genome)

•The HLA A & B genes are tightly linked on 6p, so are inherited as pairs (haplotypes)

-example: a person may have the genotype A12, B3/A4, B27 and will pass on either the A12, B3 or the A4, B27 HLA alleles; crossovers are extremely rare. -The odds that 2 children in a family will have the same haplotype combination is ¼ -the DR gene complex is also closely linked on chromosome 6q, so DR and DQ alleles are almost always inherited as a part of the haplotype also.

•Suppose stalk lodging (falling over) occurred in 10' tall plants:

-in A'A', B'B,' C'C', D'D plants, D would be identified as a recessive gene for lodging -in A'A, B'B', C'C', D'D' plants, gene A would be a recessive gene for lodging •If both 9' and 10' tall plants lodged, then D and A respectively would be identified as dominant genes for lodging • QTLs still follow Mendel's Laws

•The transposase/integrase is only expressed in developing tissues and not in germline cells.

-it is expressed during DNA replication when the DNA is still hemimethylated. -if a copy moves to an unreplicated region, additional copies can be added to the genome.

Pros and cons of using Nitrous Acid

-it is used as a meat preservative - keeps meat red -cultures with high use, especially with fish, have more stomach cancer - it can be present in some vegetables and water wells -it prevents growth of Clostridium botulinum -it is also made by bacteria in our salivary glands

Retroposons (Example: Human LINES)

-no terminal repeats and no encoded transposase -encode a reverse transcriptase -encode an endonuclease -create 7-21 bp repeats at insertion sites.

•What is the probability that a taster in this population is heterozygous?

-note there are 48 Tt :16 TT tasters, so ¾ of the tasters are heterozygous

•non-LTR retroposons are non-viral and have no reverse transcriptase

-seem to occur from reverse transcriptase copying of other RNAs -examples SINE like alu elements in humans and MITEs in plants -made by reverse transcription of RNA, 10, tRNA, 7sRNA etc -similar origin as processed pseudogenes.

miRNA (microRNA)

-these are coded by genes transcribed by RNA Pol II so get a 5' Cap and poly A tail. Even if 3-4 Kb long, activity comes from a hairpin foldback around 70 nucleotides long. The fold of the hairpin is cut off by Drosha in flies and animals or Dicer in plants producing a pre-microRNA which is then diced and functions in RNAi. Typically, miRNAs in animals do not have perfect homology with the target so are more likely to simply inhibit translation rather than slice the mRNA. They can also target some mRNAs for 'storage'.

More recently, Jensen an educational psychologist and Shockley an engineer (he shared a Nobel prize for developing transistors) argued that since IQ has a strong genetic component (H2), education could not eliminate disparities, especially as measured among 'races'. However:

-this does not account for possible interactions in the different ways individuals may learn, aural vs visual etc. -it assumes IQ scores are a meaningful measure of intelligence -it assumes culturally unbiased tests, which is very questionable -it does not appreciate that even high H^2 traits can be greatly affected by environment

Detached retina can be an example of...

-variable age of onset -phenocopy -lack of penetrance

vp mutants

-vp mutants in maize lack carotenoids so cannot survive when homozygous (vp/vp)

•Many important traits are not simply (1 gene) inherited:

-weight -height -yield in bushels per acre or milk per cow -soluble sugars or fat content -IQ, etc., etc

Tetraploid maize

-when initially created, fertility may be low but with selection, fertility can approach normal; this seems to reflect less cases of multiple chromosomes trying to pair together -functional gametes in this case will be diploid

•Genes in tandem arrays such as rDNA often have the same sequence

-with hundreds of tandem copies of rDNA genes, would a point mutation in one copy be very detrimental? Probably not, but in any case, the copies seem to homogenize to the same sequence.

How nonsense suppressors often mean a changed tRNA

. In E. coli, a mutation occurred and caused a non-functional enzyme. In in certain strains of bacteria, or as results of another mutation, the enzyme was restored to some degree. Eventually it was possible to show that in this case sense the same suppressor would work for different mutations and different genes that it was actually able to suppress a stop codon. So, the original mutation was a nonsense, and the suppressor mutation was a change in a tRNA gene that then recognized the stop codon and replaced it with a regular amino acid.

RFLP F2 mapping

. The first two lanes show the two parents, and the other lanes, except for some labeled size markers show individual F2 progeny that are homozygous like a parent or heterozygous (two bands).

rate of mutation

1 mutation in 105 to 107 gametes

Steps of translation

1. Initiation 2. Elongation 3. Termination

How to make cDNA from mRNA

1. Isolate mRNA by taking advantage of the poly A tail 2. Add oligo-dT primer 3. Add dNTPs & reverse transcriptase 4. Destroy mRNA 5. Generate 2nd. strand of DNA 6. Now use dsDNA for template 7. PCR reaction including appropriate primers and Taq polymerase and other components

Uses of Tns

1. Transposon tagging 2. Provide sequencing primer sites. 3. Make another sequence 'portable'

What is the probability that a Cc, Tt, D'D, individual will produce a: C, t, D gamete?

1/2 X 1/2 X 1/2 = 1/8 since the three traits are independent

How long does conjugation last in E. coli

100 minutes

Hydrogen bonding for pyrimidines

2 hydrogen bonds hold adenine and thymine together; one hydrogen bond linking oxygen and hydrogen, and the other linking hydrogen and nitrogen.

How many different amino acids are there for normal proteins?

20

Triplet

3 bases per codon

TET function diagram

3 types of TET that convert methylated C to C

What direction to you read anticodons?

3' to 5'

How many lacI transcriptions make a repressor protein?

4

Alternative splicing in human calcitonin gene

5 exons, 4 introns -Thyroid; exons 1-2-3-4 then poly A tail -Neurons; exons 1-2-4-5 then poly A tail -Both are made in a "pre" form that is modified to functional form

next step of intron slicing

5' end is connect in 3' end and forms a lariat and cleaved at each end

Direction of reading mRNA during translation?

5' to 3'

Which direction does DNA polymerase move?

5' to 3'

advantages of using BAC as a vector

50-150 kB inserts Stable

Rate of transcription in eukaryotes

6-70 nucleotides per second

length of tRNA

75-85 nucleotides

eukaryotic ribosomes

80S (40S and 60S subunits)

demethylation in daughter cells

90-99% of methylation is stripped at some stage of gametogenesis or embryogenesis. In humans, stripping of the male gamete occurs after entering the egg and then the new germline cells are re-stripped. Thus the methylation pattern must be re-established.

How often do human genes undergo splicing in a developmental, tissue-specific, or signal transduction-dependent manner?

95% of the time

A, P, E sites

A = next aminacyl tRNA P = growing peptide site E = exit

DNA glycosylase

A DNA repair enzyme that cleaves the bond linking a purine or pyrimidine to the deoxyribose of the backbone of a DNA molecule.

Klinefelter syndrome

A chromosomal disorder in which males have an extra X chromosome, making them XXY instead of XY.

Photolyase

A common enzyme found mostly in single celled organisms can, with the aid of blue light and FADH+, break the bond that creates thymine dimers

Codominance

A condition in which neither of two alleles of a gene is dominant or recessive.

dihybrid cross

A cross between individuals that have different alleles for the same gene

Cot Curve

A curve that indicates the rate of DNA-DNA annealing as a function of DNA concentration and time.

Cri du chat syndrome

A deletion of the short arm of chromosome 5 associated with an array of congenital malformations, the most characteristic of which is an infant cry that resembles a meowing cat.

Karyotype

A display of the chromosome pairs of a cell arranged by size and shape.

Major Histocompatibility Complex (MHC)

A family of genes that encode a large set of cell surface proteins called MHC molecules. •The MHC genes are critical to identification of 'self". Composed of MHC classes I, II, and III

Cytokinesis not occurring after mitosis

A fertilized egg from Drosophila provides an example of a coenocytic cell; multiple DNA replications and mitosis occur without cytokinesis resulting in a multinucleate cell. Coconut milk is another example. Technically, a syncytium is when cells fuse to create a multinucleate cell, as in the giant cells in plant roots infected by root knot nematodes.

TAQ polymerase

A heat-stable form of DNA polymerase extracted from bacteria that live in hot environments, such as hot springs, that is used during PCR technique

Attenuation in Tryptophan Operon

A leader on the trp operon mRNA has two trp codons before a stop codon If there are plenty of charged trp•tRNAs available, translation of the leader up to the stop codon is rapid and a transcription termination loop forms in the nascent mRNA between the ribosome and the RNA polymerase, causing the polymerase to be released If the ribosome stalls at a trp codon, an alternative loop prevents the termination loop from forming and transcription proceeds to make the full-length mRNA attenuation alters expression of the trp operon 10-fold

double fertilization

A mechanism of fertilization in angiosperms, in which two sperm cells unite with two cells in the embryo sac to form the zygote and endosperm.

time-of-entry mapping (gradient of transmission)

A method of donor gene mapping by conjugation that uses interrupted mating to determine the order and relative timing of gene transfer.

replica plating

A method of identifying bacterial colonies that have certain mutations by transferring cells from each colony on a master plate to a second (replica) plate and observing their growth when exposed to different conditions.

super repressor

A mutation in the I gene that alters its ability to bind lactose, but not the ability to bind the promoter

insertion

A mutation involving the addition of one or more nucleotide pairs to a gene.

nonsense mutation

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

If the third base of an anticodon is a U, it can pair with...

A or G

Nulli-tetra lines of wheat

A pair of chromosomes missing from one genome can be balanced by having 2 extra copies of the homoeologous chromosome from a different genome. Some of these 'substitution lines' as they are called, have a characteristic phenotype that was used with isozymes and later with DNA sequences to identify syntenic chromsomes in the different genomes.

What is a peptide bond composed of?

A peptide bond has a carbon to nitrogen bond and an oxygen attached to the carbon, and a hydrogen attached to the nitrogen

prophage

A phage genome that has been inserted into a specific site on the bacterial chromosome.

temperate phage

A phage that is capable of reproducing by either the lytic or lysogenic cycle.

F (fertility) factor

A piece of DNA that confers the ability form a sex pili.

Polypeptide

A polymer (chain) of many amino acids linked together by peptide bonds.

helix-turn-helix

A protein domain composed of two α helices joined by a short strand of amino acids and is found in many DNA binding proteins.

Luria and Delbrucks' 'Fluctuation Test'

A single E. coli cell was allowed to grow into four generations and ended up with 16 cells. T1 bacteriophages were added to the 4th generation, which causes E. coli to lyse. All bacteria should be susceptible. However, A mutation could cause the E. coli to become resistant to the bacteriophage. According to the induced theory, this could only happen in the fourth generation when the mutagen, T1, is introduced. According to the spontaneous theory, mutations can occur in any of the generations. Found that different numbers of mutated progeny in the fourth generation were found each time. This showed that the mutation were in fact random.

Base pairing

A-T/U (pyrimidines), G-C (purines)

ABO antigens

ABO antigens are modifications to red cell surface proteins The A allele-encoded enzyme adds an N-acetyl galactose to the base structure and the B allele enzyme adds just galactose. The antigens in this case are similar to plant proteins that can pass through the intestinal mucosa triggering synthesis of anti-A or anti-B antibodies in individuals who do not have those antigens.

Maize Tns are used to induce 'tagged' mutations. Ac/Ds into: Spm:

AC/DS into: •Tobacco •Arabidosis •Rice •Flax •Tomato •Carrot •also used with a promoterless 'gus' gene to detect promoter insertions Spm •alternate splicing can make 4 proteins, including a transposase •only creates a 3 base footprint •more leaky mutants are found •all subject to silencing via DNA methylation

What does DNA ligase require to function?

ATP

Translocation based trisomy 21

About 5% of trisomy 21 cases are inherited based on the presence of a translocation. Here the mother has 45 chromosomes and one of her 14's has the long arm of 21 also. She is fine but if the TL14-21 and another 21 goes into an egg, the child will have 3 21's. Observations show approx 11% of her children will be Downs, while if the TL is in the male only 3% of the progeny are affected. in theory, it could be about 50% in both cases, but most Trisomy 21 conceptions abort spontaneously and there also seems to be an affect on sperm viability.

How eukaryotes know where to start transcription

About ten bases before the start, there is highly conserved TATA box on the sense strand about 25 bases before the transcription start point, and an earlier recognitions site (CAAT box) about 75 bases before the start of transcription. In presence of a sigma factor the large RNA polymerase assembles and begins transcription.

How prokaryotes know where to start transcription

About ten bases before the start, there is highly conserved TATA box on the sense strand about ten bases before the transcription start point, and an earlier recognitions site about 35 bases before the start of transcription. In presence of a sigma factor the large RNA polymerase assembles and begins transcription.

BLAST search

Acronym for Basic Local Alignment Search Tool search; a search using shared databases that retrieves gene and protein sequences and shows their similarities among organisms.

Two theories on how mutations occur

Adaptation/Induced mutation Spontaneous/Random mutation

Alkalating agents

Add a methyl or ethyl group to guanine, which lead to mispairings. EMS is most common example, which is extremely carcinogenic.

How to increase growth rate of bacteria in media?

Add nutrients to the media

TUT (terminal uridylyl transferase )

Adds UMP to a terminus that may be created by a guide.

Normal Hemoglobin

Adult hemoglobin (Hb-A) has 2 alpha and two beta polypeptide chains Each subunit contains a heme cofactor that allows oxygen binding and transport. The chains can be separated; electrophoresis showed that only the beta chains migrated differently in HB-S and HB-A.

deletion and synapsis

•At synapsis, chromosomes pair 'gene for gene' along the length of the whole chromosome, so that it may be possible to tell that one chromosome in a heterozygote has extra material lacking in the other:

Gregor Mendel

•Augustin monk; Lived 1822-1884 •Interest in Plant Reproduction •Experimented with garden peas (Pisum sativum) •Published in 1865, but not recognized as significant to 1900

Mapping Ac or Ds

•Barbara noted that when trying to map Ac or Ds, they weren't always at the same location. •She also found that more copies of Ac led to more spots representing reversions (purple spots) in the C gene case.

What Lyon's law explains

•Barr bodies are inactive X chromosomes •Dosage compensation

MHC II

•Class II includes HLA genes Dp, Dq and Dr that are primarily expressed on immune system cells. - the a (alpha) and b (beta) subunits here are protected by a 'clip' until able to interact with an antigen that was introduced by exocytosis into an endosome (see picture on next slide) -These interact with CD4 helper T cells for activation

MHC III

•Class III includes genes for 'complement' , 20-30 circulating proteins like histamines that are critical to activation of B cells, and for other chemical responses

Genes and IQ •assuming IQ means something, are differences genetic, primarily environmental, or both?

•Cyril Burt used twin studies to conclude that H2 for IQ is highly heritable - say 78% -his studies looked for ID twins reared apart -he used dads occupation as predictor of IQ -he may have 'fudged' some of his data • We know that G X E can be substantial

If the parents are at the extremes, it is possible to estimate the number of genes segregating for the trait by the formula:

•D is the difference in the parental averages and Vg is the genetic component of the Variance.

Other ways of detecting clone sequences

•Detection of protein with a prepared antibody

P elements in Drosophila Discovery

•Discovered in 1960's when M (maternal) female lab strains mated to P (paternal) wild strains gave rise to 'hybrid-dysgenesis' where the F1s had a high frequency of mutation, aberrant ratios, sterility, non-disjunction and chromosomal aberrations. •There was no hybrid dysgenesis in the reciprocal cross, implicating a cytoplasmic factor:

Dizygotic twins

•Dizygotic (DZ) twins come from 2 eggs released in the same ovulation fertilized by two different sperm, so differences can come from both genes and environment (ranges from 2 to 40/1,000 births) depending on population and age of mom)

genetic drift

•Drift reflects chance fluctuations so is especially relevant in small populations. •Drift eventually leads to fixation, i.e., the whole population has the same allele. •The odds that A or a will be fixed if chance is the only factor equals the initial frequency of each allele in that population. •As populations become small, inbreeding is likely to occur which further leads to a loss of heterozygosity.

Duplications and evolution

•Duplications provide extra copies of potentially useful genetic information and thus can play a positive role in evolution -gene families like the globin genes allow changes in timing or level of expression to occur in one copy without losing the original copy

TALE features

•Each TALE protein has a nuclear localization signal •Each has a transcription activation domain •Each has 3-30 repeats of 33 or 34 amino acids in its DNA binding domain •The 12 and 13th amino acids within each repeat can vary; specific pairs of amino acids recognize A, T, G or C •This means a man made sequence can be generated to bind to a targeted DNA sequence with high specificity •A nuclease (usually Fok1) can be added to the TAL and will cut the double stranded DNA at the targeted site

Basic quantitative trait model

•Each gene is independently inherited. Each gene shows incomplete dominance •Every contributing allele of each QTL (A', B' , C' etc.) makes the same contribution, Gene interactions are not critical

Controlled crosses could be made between strains of mating types 'A' and 'a'

•Either can be the female or male donor in the cross depending which is put on low NH3 medium first •The products of meiosis are contained in a sac (an ascus) and can be isolated and grown after heat shock •"A" and "a" occupy the same locus but code different sequences so may be called idiomorphs rather than alleles

Examples of cre-lox use

•Eliminate selectable markers after creating transgenics; -Pioneer eliminated hygromycin resistance after use in selection of transformed callus for a gene required for pollen formation using a cre gene expressed only in seeds •Non-lethal knock out of a mouse gene that functions in osteogenesis •Conditional (temperature sensitive) inactivation of a growth factor receptor gene in mouse •Conditional KOs of bradykinin receptors to study effects on hypertension in mice

Fusarium solani vs pea or bean

•F. s. formae specialis phaseoli is virulent on common bean but avirulent on pea •Induces high concentration of pisatin in pea but little phaseolin in bean •Relatively insensitive to phaseolin but sensitive to pisatin •F. s. f. sp. pisi virulent on pea, avirulent on bean. •induces high concentration of phaseolin in bean but little pisatin in pea •Able to detoxify pisatin but not phaseolin

fungi and bacteria

•Fungi -EF-1α (translation elongation factor), β-TUB (β-tubulin), and CAM (calmodulin) •Bacteria HSP60 (or whole genome nowadays)

Gac-A and Gac-S

•Gac-A is a constitutive activator component that if phosphorylated by the Gac-S sensor tuns on transcription of several gene that encode alternate sigmas -Hrp-L used for synthesis of effector molecules to be secreted into the host -Rpo-S activate transcription of genes that make secondary metabolites -Rpo-L for non-coding regualtory RNAs • So far, the only known basis for Gac-S to trigger the cascade is 'stress': the bacteria must switch from motile to sessile and suppress host defenses

genetic blocks

•Garrod correctly speculated that the genetic blocks were related to missing steps in metablolism due to the lack of a biocatalyst, or enzyme in modern terminology.

CRISPR in insects and animals

•Gene added to mosquitoes to prevent malarial pathogen reproduction (gene drive* too) •Alter a defective muscle gene in to a less harmful version of DMD (has worked in mice) •Remove T-cell receptor that is targeted by the AIDS virus (mimics a natural mutation) (China ! In vivo)) •Sickle cell editing on hematopoietic stem cells that can be returned (mouse model < 5% needed) •Same for blood clotting defects

Gene writing format

•Genes or alleles are in italics, while proteins are not: lexA codes for LEX A protein, even if the word protein is not present.

Conidiation info

•Genomic sequence information is available, as are maps and many mutant stocks. •Studies reveal that common signal transduction pathways function, with gene expression regulated by interaction with several environmental factors. •Timing of conidiation is also regulated via circadian rhythms which involves clock genes, for which mutants are also available

HLA genes affect tissue transplants

•HLA A, B and DR alleles are critical to successful tissue transplants for hearts, kidneys, skin and livers, but not to tissues such as a lens for the eye. •An individual will reject any tissue that has an allele that is not present in his/her own tissues. •There are hundreds to thousands of different HLA alleles!

Critical considerations about heritability

•H^2 estimates are only good for the population and environment in which they are made! •H2 is only measuring genes that are segregating or differ in individuals in a population; if all are homozygous for genes that affect a trait, those genes will not contribute. For example if one sorghum cross was A'A', B'B' CC, DD by A'A', B'B', CC, DD and another was A'A', B'B' CC, DD X AA, BB C'C', D'D' we would see very different estimates of heritability, even though there are 4 genes that can contribute to sorghum height . •Even traits that all 'all or none' can be the result of cumulative gene action. -If a threshold of contributing alleles is reached, the individual is affected -In different families, segregation of different genes may trigger the threshold value H2 will change over generations if selection is practiced

Polyploidy occurrence

•Having more than 2 sets of chromosomes is very rare in animals •A couple of frog species like this tree frog are tetraploid.

Different classes of mutants in C. elegans

•Heterochronus mutants cause 'miss-timing' -example lin-14; vulva starts developing too soon •Transformation mutants causes the wrong tissue to develop -unc-86; too many cells become neurons and the worm is un-coordinated •Segregation mutants occurs when both daughter cells follow the same developmental fate -in lin17 mutants, one daughter cell does not undergo PCD so no distal tip is made •Execution mutants divide in the wrong plane -in lin11 mutants, vulva development is abnormal since 10 and 2ndary cells aren't defined •Overall, 113 cells are fated to undergo apoptosis. Failure leads to slow movement and other problems that would not allow survival in nature.

Hypothesis of eRNA

•Hypothesis 1: Transcription of the eRNA allows chromatin remodeling •Hypothesis 2: The eRNA itself has a direct role in regulating transcription

telormeric or subtelomeric centromeres

•If chromosomes with telomeric or subtelomeric centromeres fuse, or if a bi-armed chromosome separates to form two one armed chromosomes, the event is referred to as a Robertsonian translocation.

Changing allele frequencies via mutation

•If we start with all AA individuals in a large population and one gamete carries a mutant a allele, we no longer have p= 1. However mutation rates are typically in the range of 1/10^6, so changes come very slowly!

cytochrome oxidase I mitochondrial gene

•In animals, the sequence of the cytochrome oxidase I mitochondrial gene is relatively species specific -can be amplified using conserved primers -lack of DNA repair increases mutation rate -coding requirement prevents too rapid change

Crowd sensing

•In many fish species if there is no male, a large female will become a functional male •In some cases they can change either direction, including typical sex coloration patterns as seen in angelfish

rbcL and matK genes

•In plants, the chloroplast rbcL and matK genes are relatively species specific

quelling

•In some fungi, extra copies of a gene can also silence the normal copies -'quelling' as described in Neurospora (but only after meiosis)

Ideal situation for mapping QTLs

•In the ideal situation a large F2, backcross or recombinant inbred population made between contrasting parents can identify regions where contributing alleles are located throughout the genome. You can: -score the entire population for 'genes' along all chromosomes; the parental allele associated with positive alleles will have a higher average value than those with the non or negatively contributing alleles -score only the extremes, as they should also have more contributing alleles at many sites Data may not be relevant to other parental crosses!

Increased ploidy

•Increased ploidy often produces showy flowers and thicker stems but does not alter the plants overall appearance. -examples include: 2N and 8N strawberry, octoploid dahlias

homozygous for an inversion

•Individuals homozygous for an inversion are typically fertile and produce 'normal' gametes with the same inversion.

Mimics of cytoplasmic inheritance

•Infectious heredity; caused by a virus or microbe that can pass through the female but not sperm -mouse mammary tumors were found to result from a virus that could be passed from the mother to her pups via the milk -CO2-sensitive Drosophila are the result of a virus that be egg-transmitted -'Killer' a particle in paramecia can be passed through the cytoplasm from a K_ individual when extended matings occur. If the recipient is kk, the 'particle' unwraps and releases viruses that kill that host. The ribbon-like particle is actually the product of a symbiotic bacterium.

Inversions new linkage

•Inversions create new linkage associations and are sometimes detected by alternate maps for two strains of the same species

Large homozygous deletions

•Large homozygous deletions are likely to be lethal.

Critical concepts

•Metabolism is a stepwise process •Almost every step requires a unique enzyme Mutations create genetic blocks and thus missing enzymes (failure to make needed compound as in ablinism, or piling up of precursors as in PKU and Alcaptonuria)

Migration- Gene Flow

•Migration cannot change the frequency of alleles in the entire species, but can affect local populations •Migration often is a sporadic occurrence, so cannot be calculated as a predictable changes of gene frequencies over time. •Migration can introduce new alleles into a population •Migration tends to homogenize populations and to prevent new species from evolving •Even one migrant with a different allele creates 'gene-flow' and prevents fixation of the common allele •Migrants may not integrate into the new population for some time

monozygotic twins

•Monozygote (MZ) (Identical) or one-egg twins have the same genotype, so differences seen must originate from environment (～ 1/1,000 births)

degenerate

•More than one codon often has the same meaning (1 to 6 codons/amino acid)

hemaphroditic plants

•Most have perfect flowers, with pistils and anthers in each flower. Ex. Peas. •Some are monoecious, with male and female flowers separated on the same plant. Ex. Maize. •Some are dioecious, with male and female flowers on separate plants.

Normal cells

•Normal cells in most eukaryotes contain two whole sets of chromosomes so are '2N' or diploid, where N represents one full set of chromosomes. Gametes should have one set so are haploid or monoploid

H-W equilibrium considerations

•Note that failure to follow random mating does not force gene frequencies to change, but can alter the genotype frequencies •If a population is random mating, even for just one generation, the genotype frequencies of autosomal gene 'A' will become p^2 AA : 2pq Aa : q^2 aa. A population where this is true is said to be in HW equilibrium.

Oenothera's built in genome conservation

•Oenothera plants (wild buttercups or pinks) have evolved so that 'good' gene combinations can be preserved. -in some of the species, all 7 chromosomes have arms that differ via reciprocal translocations. (others have only 5, etc) -this results in "Renner" complexes, so that any crossover gametes will be eliminated and linkages will be conserved -only parental allele combinations can segregate into viable gametes -limits prospects for evolution, but seems to have succeeded

ROS

•Often earliest detected induced response Direct anti-microbe effects & signaling •Response follows change in ion flux in membrane (K+, Cl-) •KO of apoplast peroxidase increases susceptibility and disease •Involved in Salicilyc Acid and Ethylene signaling (so SAR potential) •Can trigger Programmed Cell Death (PCD or apoptosis)

oxidative deamination example

•Oxidative deamination of A to I via ADARs (adenosine deaminase acting on RNA) -Occurs in double stranded regions, foldbacks or guides

Mispairing between duplications

•Pairing in heterozygotes is like that in deletions; the extra material bulges out •Mis-pairing between the duplicated sequences in meiosis can lead to unequal crossing over and increase/decrease the number of copies

meiosis for individuals heterozygous for inversion

•Pairing of chromosomes in meiosis of individuals heterozygous for an inversion requires looping and twisting to match homologous sequences. -small inversions may just lead to an unpaired area •A crossover inside the inversion loop gives defective gametes, so recombination appears to have been prevented.

CRISPR in plants

•Pioneer: maize increase amylopectin in seed starch by knocking out Wx1 gene •Pioneer: substitute promoter for ARGOS8 give reduced ethylene sensitivity and improved grain yield under drought stress conditions •Downy mildew resistance in lettuce •Alter morning glory flower color

Plant defense

•Plants do not make antibodies (unless engineered to do so) •Single gene resistance typically involves "R" genes that encode a protein with a Leucine Rich Repeat (LRR) and Nucleotide Binding site (NB or NBS)

methylation in embryonic development

•Prior methylation patterns are erased early in embryo development (blastocsysts) •Underlying base sequence and trans-acting factors important in re-methylating •Histone modification can also guide sites of methylation (but they also are affected by DNA replication) •In plants small interfering siRNAs seem can also invoke RNA directed DNA methylation (RdDM), especially targeting Transposons and transgenes.

Sigma Factors in Pathogenic Bacteria

•Pseudomonas sp. can cause disease in plants & animals •They have '2-factor' systems that regulate production of sigmas for genes required in infection

Fire and Mellow's work with C. elegans (nematode) 1998

•RNAi was described in 1998 by Fire and Mellow based on work with C. elegans, a nematode -Attempted to use injected antisense RNA to 'knock out' expression of a specific gene -Found that a control made of dsRNA worked even better than the antisense strand -Later found could feed the nematodes bacteria expressing a ds region (designed to form a hairpin after transcription) of a nematode gene to knock down that gene's expression -Received Nobel Prize in 2006

How to identify a cloned sequence

•Sequence homology to known genes •Expression when possible •Detection of protein with a prepared antibody

temperature basis for sex determination

•Snapping turtles: <69°F females 69-72°F, either >72°F males •Crocodiles: high or low, all female; in-between, all male •Daphnia: temperature regulates some of the same genes involved in sexual development as in Drosophila, such as Dsx (doublesex)

Sorghum height

•Sorghums native to Africa are about 10 feet tall •Sorghum grown by US farmers is closer to 2' tall -sometimes called '4-dwarf' or 'combine' sorghum or milo -introduced lines are 'converted' to dwarfs and to mature in our environment independent of day length

Inactivation during gametogenesis

•Specific regions of non-sex chromosomes are inactivated during gametogenesis so are not expressed in the fertilized egg or resulting cells until the inactivation marks are removed.

The simplest systems

•Spore formation in Bacillus subtilis -uses different sigma factors with unique promoter sequence targets 6 vegetative and 4 spore forming sigma's have been identified

T-cell Features

•T cells mature in the thymus; any that would bind to self antigens are eliminated •T cells must recognize the antigen presented and that it is on a 'self' B cell; •They express T-cell surface receptors made by 4 genes that are like the antibody H and L chain genes, but with fewer V and J segments; •The T cell receptor genes are labeled TCR A, D, & B & G -The D gene on chromosome 14 is entirely within the A gene; the D gene is rearranged first and expresses a protein called d -When the A gene rearranges to produce the a protein, the entire remaining D is cut out -Likewise, the B and G genes on chromosome 7 are expressed G first (g), then B (b)

Other lessons from nematodes

•Temperature sensitive mutations allow the discovery of when genes function -Zyg9ts affects development only if heat is added between 52 and 70 minutes - •Removing either of the first division cells means no development -cell fate is set at the first division; no new cells are 'stem cells' - •Most larval cells do not divide again • •131 cells undergo natural cell death (apoptosis) - •Around 150 microRNAs function to regulate 7% of gene expression via RNAi

Eugenetics details

•Term coined by Francis Galton, 1883 •Gained popularity as knowledge of genetics increased •Applications to animal breeding showed gains by selection

Mapping QTLs

•The actual identity of genes/alleles the contribute to quantitative traits has seldom been known, but that is changing ! •Now that RFLPs, SNPs, AFLPs, SSRs and other DNA based-polymorphisms as well as DNA sequencing (WGS, Rad-SEQ etc) can be used to detect differences throughout the genome, tags in or closely linked to QTLs can be identified.

C. elegans unusual features

•The chromosomes do not have classic centromeres, but are 'diffuse', meaning they are pulled apart at multiple sites. •The genes are often transcribed in a polycistronic fashion, but then in processing, the specific coding regions are separated and a 5' leader, coded elsewhere, is added to enable translation. The 5' signal on the individual mRNA needed for adding the leader is referred to as an 'outron'. •C. elegans adults can be males (XO) or hermaphrodites (XX) -Hermaphrodites can self fertilize

MHC I

•The class I genes include Human Leukocyte Antigens HLA A, B and C that are expressed as glycoproteins on almost all cells after processing in the ER. -a (alpha) and b (beta) subunits, if bound to an antigen, are moved to the cell surface and recognized by CD8 receptor class of T cells. (also called Killer T cells since they can induce apoptosis in infected cells) -for 'presentation' on the cell surface a TAP (T-cell activating protein) complex creates a pore

different types of antibodies (immunoglobulins) Class switching can occur: if you go back and look at the 'C' region in the previous slide you will see that the a, b g etc can all be added to the same variable portion.

•The classes are named based on the H chains -IG g (gamma globulin) ~ 80% •targets viruses, bacteria etc •only antibodies able to cross the placenta -Ig M recognizes cell surface antigens ~7% -Ig A secreted in saliva, tears, milk (esp. colostrum) ~12% -Ig D mostly stay on B cells -trace -Ig E high in individuals allergic to stings, venom -trace •these reflect the CH components of the previous slide

Dihybrid cross with genotypes

•The cross was: YY, RR x yy, rr (both true breeding, homozygous) •The F1 progeny were all Yy, Rr double heterozygotes •Each gamete from the F1 had either R or r and Y or y •That means the gametes could be RY, Ry, rY, or ry, 1/4th each •The F2 phenotypic ratio in this case is: -9/16 R_, Y_ (round, yellow) -3/16 R_, yy (round, green) -3/16 rr, Y_ (wrinkled, yellow) -1/16 rr, yy (wrinkled, green) •The results told Mendel that the two genes behave independently

number of chromosomes

•The number of chromosomes in a set is a species characteristic (N = 23 in humans, 10 in maize, etc.) -If doubling of chromosomes is known to have occurred in the past, X rather than N is often used to define the ancestral number of chromosomes in the original set.

gene flow and crops

•There is concern that genes introduced into crops may flow into relatives; for example if a gene for Roundup resistance was added to sorghum it could also end up in Johnson grass, a related weed species. Weedy red rice can cross with rice and introduce unwanted genes.

Maternal Effects

•This occurs when a substance deposited in the egg affects development of the progeny, no matter their own genotype. •A classic example is the direction of shell-coiling in the snail, Limnea peregra.

Retroposons and non-LTR retroposons

•Together these may be > 50% of the genome

Translocations

•Translocations are reciprocal exchanges created when the broken ends of two different (non-homologous) chromosomes are healed by joining. •If the breaks do not disrupt a gene or alter its regulation, there is typically no associated phenotype. •Homozygous normal or homozygous translocation chromosomes pair and segregate with no problem in meiosis.

How point mutations can revert back to wild type

•True reversions to the original base sequence •Second site suppressor mutations •Nonsense suppressor mutations

Inversion phenotypic effects

•Unless the breaks damage a gene or the switch puts a gene under control of a new promoter, there is unlikely to be an associated phenotype.

Sources of variation

•VT (total) or VP (phenotypic) are used to describe the variance when both genes and environment contribute to variation. Vg is the genetic component and Ve, the environmental. Vgxe allows for the fact that some genotypes may perform differently in different environments, but it is very difficult or impossible to measure every possible combination (norm of reaction). Consequently, breeders tend to stick to one breed in a common environment in order to get some measure of Vg and Ve.

Vg is sometimes broken down into

•Vg is sometimes broken down into VA (additive effects), VD, (dominance effects) VE (epigenetic effects) etc. to define different type of interactions that cause variation.

Methods for estimating h^2

•We saw last time how crosses between purebreeding plants or inbred animals can be used to determine heritability. Estimates can also be made based on relationships. •Correlations among relatives and Covariances for traits can also be used with 'paired' observations

founder effect

•When a new population is initiated from one or a few individuals, it is called 'founder effect' and again an allele that was rare overall can become common.

How many genes contribute?

•When environmental effects eliminate the stair-steps produced by genotypes, it can be very difficult to estimate the number of genes that contribute to a trait.

Mitotic recombination as a tool to study development

•X-rays can induce a high frequency of mosaics as a result of mitotic recombination in heterozygous flies. -In the case of the minute gene, it is clear that each homozygous cell is autonomous in expression of the gene. -X-rays later in development lead to smaller segments of wing that are affected (homozygous recessive) this can cause a small scalloped segment along one edge.

Defective Sry gene

•a defective Sry gene gives Swyer syndrome, female phenotype but sterile and lacks estrogen production so benefits from hormone treatment

cystic fibrosis

•about 1 in 24 in that population is heterozygous ( Cf/cf where Cf_ are normal and cf/cf are affected) •Thick mucous clogs lungs and also prevents secretion of digestive enzymes from the pancreas •very prone to infections •survival has improved from <2 years in 1939, to 4 in 1950 to 12-16 in 1968 to an expected 40 or > for those born in 2000 males are infertile;females may reproduce with modern technology

papillae

•accumulations of lignin and callose inside the cell at the point of attack intracellular depositions of lignin and callose that often Impede further development by fungal pathogens

pig organs for humans

•alter the pig cell antigens -knock out a gene for making galactose so it can't be added -knock out all 62 porcine endogenous retroviruses (PERVs) at once (UC Davis) •replace pancreas genes in embryonic stem cells with the human versions -re-implant and identify chimeric pigs/pancreas

Avidin and Biotin linked assays

•avidin and biotin have affinity coefficient around 10^-15 •one protein or compound connected to biotin, the other to avidin will 'find' each other

WRN

•defective in Werners syndrome which causes premature aging. The protein it encodes is a helicase that interacts with a number of other proteins involved in DNA repair

Duplications

•duplications involve added copies of DNA sequences in a chromosome -most are tandem duplications, such as A-B-C-•-D-E-D-E-F etc. -sometimes there are inverted repeats or ectopic insertions at a new location •In some cases, as will be shown, extra copies of a gene affect phenotype

ATM

•gene involved in repair of broken DNA; if it is defective, the individual has Ataxia-telangiectsia and an increase risk for cancers such as leukemia, especially if exposed to radiation.

SNRPN

•is silenced in female oocytes; failure of the male copy of the gene in the child leads to Angelmann syndrome (once called happy-puppet syndrome)

mRNA response to hormones

•mRNAs stabilized when the hormone is present -Vitellogenin mRNA in frog liver with estrogen has 500 hour half life versus 16 without -Casein mRNA in rat mammary has 92 hr half life if prolactin is present, vs. 5 hr without

Recessive mutation examples

•p53 2X 10-7/bp/gen •Retinoblastoma 8 X 10-6

more examples of bottleneck/founder effects

•recall the use of one source of CMS, (Texas cytoplasm) in maize breeding leading to a monoculture situation as far as leaf blight susceptibility. •many examples exist where a high yielding crop variety is so widely planted that there is virtually no genetic diversity: once a new pathogen evolves, all plants are susceptible. •In 2004 experiments were started on several small Islands where prior anole populations were eliminated by a hurricane. One mating pair was placed on each island and the expanding populations are being monitored for adaptation to each islands vegetation. •More than one bull selected for use in artificial insemination of dairy cows has been discovered to carry a detrimental recessive. Some of these were uncovered by use of DNA CHIPS to show that certain regions in Holsteins, Jerseys, and Brown Swiss were never homozygous.

Exception to this idea

•there are also cases where asexual reproduction occurs in higher organisms: -Some lizards and even turkeys can have parthenogenic reproduction, where the chromosomes of unfertilized eggs double and lead to viable organisms

Denfensins

•these are peptides with 45-54 amino acids that are often in seeds, secreted from roots, etc. that have antifungal activity: •all have 6-8 cysteines at conserved spacing •they are often made constitutively, but also are induced on exposure to a pathogen •they interact with negative charges on the microbes membrane and cause pores, leakage and death Defensins are also active against some human pathogens. Some are expressed in many tissues and some are very specific: In corn, ZmES1-4 is exclusively expressed in the female gametophyte (Amien et al., 2010), while ZmESR6 is expressed in the endosperm of immature kernels. Human defensin HBD2 expressed in A. thaliana rendered plants more resistant to the 3 pathogens tested.

altering T cells to treat cancer

•three changes made in human T cells from cancer patients: -1) add gene to recognize a cancer cell specific epitope -2) remove a gene that might block the interaction -3) add a gene that prevents the cancer cell from inactivating the T cells clinical trials underway

Apomictic plants

•unfertilized eggs double to produce viable diploids -In some cases pollen must be present but does not fertilize the egg -In some cases, there may be a mixture of apomictic and normal seeds

Important things to know about Phytoalexins

◆ Broad-spectrum antimicrobial activity ◆ Localized in the area of HR (Hypersensitive Response) ◆ In many plant-pathogen interactions, associated with HR ◆ Most are chemically related to known classes of secondary metabolites that also can accumulate constitutively (e.g flavanoids, terpenoids) ◆ Members of same plant families produce phytoalexins that differ, but fall into the same chemical class

Cellular responses associated with the Hypersensitive Response (HR) cell death

◆ Rapid production of ROS (not sufficient to kill cells) ◆ Production of phytoalexins ◆ Biosynthesis of hydrolytic enzymes ◆ Pathogenesis-Related (PR) proteins ◆ Protease inhibitors ◆ Cell wall strengthening ◆ Production of signaling molecules: Nitric Oxide (NO), Salicylic Acid (SA), Jasmonic Acid (JA) and Ethylene Programmed cell death (PCD) may also occur. In plants, both the mitochondria and chloroplasts seem to show early signs of PCD, ETI can induce SA. While low SA prevents cell death, high levels at least in Arabidopsis lead to PCD with several receptor and other gene products involved; it's not just a case of high levels of ROS.

competent bacteria

bacteria capable of absorbing naked DNA

tyloses

balloon-like ingrowths of xylem parenchyma into the lumen of the xylem vessel, may also be a site of accumulation of toxin phenolic compounds

The problem with just removing histones as a mechanism for enhancing gene expression

because it is done selectively for specific genes and not others, as demanded by developmentally expressed genes, tissue specific gene expression, etc.

Why did it take until 1950 to use bacteria for genetic studies?

because it wasn't until 1950 that the mechanisms of gene transfer were discovered

bicoid mRNA

bicoid mRNA has a region at the 3' untranslated end that has a 50 base hairpin recognized by a maternal protein called Staufen that gets it onto the dynein for transport to the correct pole

U2

binds to U1 and attaches to an intermediate A and start folding the intron

AGO4/PIWI in plants

binds to siRNAs made from transposon coded mRNA to form RNA-induced transcriptional silencing (RITS) complexes which then guide RNA-directed DNA methylation of C in CG, CAG, CTG, CCG etc sites using DRM2 a "domain rearranged methyl transferase"

Prior methylation patterns are erased early in embryo development by...

blastocysts

how a transgene hairpin is introduced

by a modified virus or transformation with a plasmid; if with a virus it is called VIGS for Virus Induced Gene Silencing Both RNA and DNA virus systems have been developed for transient knockdown of target gene expression systems

How bacteria protects itself from restriction nuclease

by putting methyl A or C

germline mutation

can be passed on to the next generation through gametes and meiosis

Protein X

can bind to the 3' tail of some messages to inhibit the interaction of the eIF4 and the poly a tail to prevent the normal loop from forming to prevent translation.

reactive oxygen species and 'heat'

can lead to removal of a base from the deoxyribose-P backbone in DNA, creating an AP site (AP can be apurinic (most common) or apyrimidinic)

maintenance methylase (DNMT1)

can methylate the symmetric C after DNA replication of a mCG •Identifies new and old strand immediately after DNA replication •Preserves level of gene expression after cell division

DNA methylation; 5mC works to...

can prevent transacting factors from binding a gene can also recruit other molecule that have to do with changing histone arrangement to open up the gene

base analogs

can substitute for purines or pyrimidines during nucleic acid replication Bromine is most common base analog.

Induction

catabolic pathway or breakdown pathway

How SOD breaks down ROS

catalyzes the rapid dismutation of superoxide radical to H202 and water

acridine dyes

cause frameshift mutations by intercalating between purines and pyrimidines. They fit into the double helix, tricking DNA polymerase by making it think there is a base where there isn't one.

defective STE gene

causes sterility

Cdc genes

cell division cycle genes, at low temps CDC mutants will go through cell cycle but at high temps they arrest

G2 is a checkpoint for...

cell size DNA replication

G1 is a checkpoint for...

cell size nutrients growth factors DNA damage

Drift

chance fluctuations that occur when the population is small

transverse mutation

change of a purine to a pyrimidine or vice versa

M phase is a checkpoint for...

chromosome attachment to spindle

plasmid

circles of DNA that replicate autonomously

Enhancer/Suppressor-Mutator

cis Determinants for Excision- : Approx. 180 bp at the 5' end and 300 bp of 3' end represent cis determinants. Contained in these regions are reiterations of a 12 bp sequence motif that is recognized by TNPA protein with 6 motifs present at 5' end and 8 at 3' end. Trans-factors: TNPA and TNPD (transposase complex) TNPD & TNPA TNPA brings the two ends together and causes DNA bending, TNPD cleaves En/Spm Transposable elements. Expression is low due to poor promoter and DNA methylation

mitotic recombination in flies

classic example of a case in flies involving a yellow and singed recessive alleles that can be seen as patches on the flies body. (next slide) Only when a crossover occurs between a gene that is heterozygous and its' centromere, can homozygous daughter cells with opposite alleles be detected.

How can competence be induced?

cold shock, osmotic shock, or electroporation (making holes in membranes)

pUC19

common cloning plasmid vector

VWF domain

common feature that appears to be involvement in multiprotein complexes

Deamination of 5MC

commonly found in CG dinucleotides in eukaryotic promoters creates T, resulting in a T:G 'mismatch' pair and triggers repair

U5, U4/U6

complex added to U2

Trisomy 21

condition in which an individual has three number 21 chromosomes, resulting in Down syndrome

Leader portion of prokaryotic mRNA

contains a consensce sequence of AGGAGG... about 8 bases before start codon AUG (Shine-Dalgarno (SD) sequence)

TET proteins

convert 5MC to 5 hydroxyMC- to formylMC- to carboxylmethylcytosine, which can then be replaced by C using Base Excision Repair (BER) or Thymine DNA Glycosylase (TDG)

Bacteriophage Lambda as a vector

could inject itself in host bacteria. Can remove section of DNA that codes for lysogenic cycle as it is not needed. This results in left and right arms that contain all the genes needed for replication but are too small for packaging.

thymine dimers

covalent link of adjacent thymine bases in DNA mostly caused by UV radiation. On replication, the ability to pair with A is lost and if not repaired, a non-A nucleotide may be included in the new strand

Oxidative deamination of C to U in DNA

creates a U:G mismatch that may be repaired to C:G (OK) or T:A (mutant) (reactive oxygen species, generated for example in mitochondria, can cause oxidative deamination of DNA bases A, G & C)

cytosine deaminase

creates a mis-paired TG followed by repair to demethylated CG

Holiday Junction

cross-shaped structure that forms during the process of genetic recombination, when two double-stranded DNA molecules become separated into four strands in order to exchange segments of genetic information.

mitotic recombination

crossing over that occurs during mitosis

industrial melanism

darkening of populations of moths over time in response to industrial pollution darkening the trees due to soot

DNMT3A and DNMT3B

de novo methylases that are critical in embryonic development in mice

Genetic Heterogeneity and Multiple Alleles lead to...

defective collagen and multiple phenotypes

Achondroplasias

defects in bone formation leading to dwarfism as seen in creeper fowl, bulldog in the Dexter breed of cattle and humans

chitinases

degrades chitin in the fungal cell wall. The plant degrading pathogen cell walls, instead of vice-versa.

B-glucanase

degrades glucans in fungal cell walls.

position effect

dependence of the expression of a gene on the gene's location in the genome (bar eyes)

Northwesterns

detecting RNA and protein interactions

northern blots used for

detecting RNA with a DNA probe

dsRNA

double stranded RNA

chromatin looping

eRNAs induce chromatin looping and transcriptional activation. Stimulus-induced expression of eRNAs cooperate with transcriptional cofactors such as Mediator and Cohesin to promote chromatin looping and transcriptional activation. They can be very long and act at sites a long way from the initiation site for transcription.

Selection allows living organisms to adapt to continuously changing environmental conditions

earth one had very little O2; now it is about 21% of the atmosphere temperature fluctuations do occr, even without man's input mutations to antibiotic resistance allows spread of pathogens

mutation in promoter

eliminates production of repressor proteins capable of binding the operator results in constitutive (continuous) synthesis of Z, Y and A proteins (regulator constitutive)

Point mutation in Z, Y, or A

eliminates the function of that section

lacZ

encodes B-galactosidase

XIST gene

encodes an RNA that binds to and inactivates the X chromosome

lacY

encodes lactose permease

lacA

encodes transacetylase

enhancer RNA (eRNA)

enhances protein production when gene is turned on

p53 gene

ensures all checkpoints are accomplished before going for S to GII. Can delay cell division or signal for apoptosis. Also involved in see if telomeres are too short.

β-galactosidase

enzyme that breaks down lactose to form glucose and galactose

exonuclease

enzyme that cleaves off nucleotides, one at a time

Cosmids

essentially the cohesive ends of Lambda with a cloning site and a selectable marker; rifampicin resistance in this case Only fragments that place the cohesive ends (cos sites) at the proper distance can be packaged into functional particles for insertion into host cells.

Segment polarity genes

establish anterior-posterior gradient within each segment These 17 known genes are expressed within segments and are regulated by pair rule genes while and after nuclei become cellularized. A homozygous defect in one of the these genes gives 'mirror image' segments.

Psuedodominance

expression of a normally recessive allele owing to a deletion on the homologous chromosome

cotransformation frequency

extremely rare (1 in a million)

Pleiotropy of OI

eyes, bones, skin etc. can be affected

Nondisjunction

failure of chromosomes to separate in MI or MII can lead to eggs and sperm with abnormal numbers of sex chromosomes

vectors

for transferring cloned DNA to another cell and short man-made DNA sequences

enzyme dicer

fragments the dsRNA (using ATP) into 21-25 bp pieces with a 2 bp stagger at each end (Drosha is an alternative to dicer in Drosophila and animals)

How to pause the log phase in bacteria

freeze them

Actinomycin

from streptomyces bacteria intercolates into DNA and prevents transcription and induces apoptosis when combined with some immunotoxins so has use in anti tumor treatments.

Point mutation

gene mutation in which a single base pair in DNA has been changed

global changes

general changes that apply across all situations or domains

types of transduction

generalized and specialized

holandric genes

genes located only on the Y chromosome •only in males, and are passed from father to son

Oncogenes

genes that cause cancer by blocking the normal controls on cell reproduction

Homoeologous genes

genes those that code for the same product but come from different genomes

CDC mutants

get stuck at a particular point in the cell cycle

Anticodon

group of three bases on a tRNA molecule that are complementary to an mRNA codon

Traits measured could be pairs of heights of fathers (Xi) versus sons (Yi) etc. The correlation 'r' can be calculated from the data, then

h^2 for offspring and 1 parent = 2 • r h^2 for first cousins = 8 • r H^2 for identical twins = r H^2 for sibs = 2 • r

Autopolyploidy

have extra copies of the same genome. For example, tetraploid maize has 4 sets of 10 or 40 chromosomes per somatic cell

Inborn Errors of Metabolism Garrod (1909)

he described several inherited traits he saw in patients that seemed to follow the then recently rediscovered Mendel's Laws

Kunitz domain

helps prevent protease degradation of the protein

Mutation

heritable change in the genetic information

most highly conserved chromosome component

histones

Zygonema

homologous chromosomes begin to pair

two types of double strand break repair

homologous recombination non-homologous recombination

Main difference between eukaryotic and prokaryotic translation

how initiation is accomplished

advantages of using YAC as a vector

huge inserts

Vectors for the two components of the Yeast 2-hybrid technique

if bait and target interact, then lacZ is activated

independent events

if events A, B, C etc are not influenced by each other the are independent and the P(combined events) = P(A) X P(B) etc Use coin flips as an example.

Cyclosporin

immunosuppressive that is often used in organ transplant patients

Conjugation pili

in a bacterium, elongated, hollow appendage used to transfer DNA to other cells

Variable expressivity example

in humans involves 'osteogenesis imperfecta' (OI), the mildest extreme being blue sclera which is shown here. Other individuals might also have loss of hearing all the way to bones so fragile that normal activities are impossible.

Lyon hypothesis

in mammals: 1) Early in embryology (< 16 days), every extra X > 1 becomes condensed and inactive. 2) Which X is inactivated in an XX cell at the time of inactivation is pure chance, but due to slower replication, the same X is inactive in every mitotic daughter cell.

disadvantages of using plasmids as a vector

in order to get plasmid into bacteria, the membrane must be disrupted. Can use an electroporator

When does the repressor protein bind to the operator?

in the absence of lactose

Barr bodies

inactivated X chromosomes found only in females

ribosome-inactivating protein

inactivation of non-host ribosomes.

variable expressivity

individuals with the same genotype have related phenotypes that vary in intensity

dominant lethal

inheritance pattern in which an allele is lethal both in the homozygote and the heterozygote; this allele can only be transmitted if the lethality phenotype occurs after reproductive age

osteogenesis imperfecta

inherited condition of deformed and abnormally brittle bones

Types of suppressor mutations

intragenic and intergenic

two types of signals to end transcription in prokaryotes

intrinsic and Rho dependent stops

BRCA1

is involved in DNA repair, especially of double strand breaks as might be caused by ionizing radiation. Women who inherit a defective copy have a high risk of breast and ovarian cancer.

Protein Purification

isolation of gene product polyhistidine tagging (His-tagging) isolation of protein by metal ion resin

How dominant and recessive alleles are represented if neither allele is dominant

it's best to use another designation and all genotypes must be defined in the legend

Two forms of 5-bromouracil

keto form (most common) and enol form

C-value paradox

lack of correlation between genome size and the biological complexity of an organism

Phases of bacterial growth

lag, log, stationary, death

advantages of using cosmids as a vector

large inserts

Mendel's First Law

law of segregation

reduced penetrance

less than 100% of the individuals possessing a particular genotype express it in their phenotype

Banded chromosomes

make distinction possible Giemsa or G banding and Quinacrine or Q banding were the most commonly used dyes. The light areas in G banding are typically euchromatin, ie 'genes' with higher GC ratios

Mutation in the operator

makes it non-recognizable to the repressor results in constitutive synthesis of Z, Y and A proteins. (operator constitutive)

second promoter of lac operon

makes one long mRNA that encodes B-Galactosidase, permease, and trans-acetylase

Where are F factors usually found?

males

Gene mapping formula for linked genes

map distance = f(NPD) + ½ f(TT)

nonsense mutation in lac operon

may also have a 'polar' effect, reducing levels of subsequent enzymes

F factor as a episome

meaning it can enter and replicate with the hostchromosome. Entry is by a single cross-over between homologous regionsin the F and the chromosome.

Ways to regulation miRNA production

methylate C's in the promoter preventing transcription of miRNA gene reducing poly-A tail to induce degradation Drosha and DGCR8 work to increase or decrease stability of miRNA

in some cases being 'different' is a disadvantage

mimic butterflies that do not resemble a toxic form female flies ignore a male with a non-standard courtship ritual

M phase

mitosis and cytokinesis

antimicrobial proteins

mode of action unknown - often present in seeds sormatin in sorghum thaumatin-like proteins

degrees of freedom

n is the degrees of freedom for the test; 0.05 is 95% confidence, etc. If the calculated value would occur less that 5% due to chance fluctuation, we say the data support the hypothesis at the 95% level.

How miRNA is produced

ncRNA transcripts that are processed to make microRNAs (nc = non-coding) miRNAs can also come from introns of other coding genes. Initial processing occurs in the nucleus but in animals is completed in the cytoplasm.

result of super repressor

no ZYA mRNA made

random mating

no selective mating in which animals chose mate depending on phenotype

ncRNA

non-doing RNA; doesn't code for proteins, but may modify proteins that regulate gene expression such as miRNA

genetic lethal

not necessarily dead, but can't pass on genes to next generation

Where is DNA stored in a eukaryotic cell?

nuclear membrane

When can homologous repair occur?

occur if a DNA strand matching the sequences flanking the break are available

somatic mutation

occur in body cells and pass to daughter cells via mitosis

Inversions

occur when two breaks in the same chromosome are repaired incorrectly

Mitochondrial transcription and translation

occurs in mitochondria as single large RNA molecule which is then cleaved; no introns; use different polymerase with different mutation rate and less repair --> more mutations

specialized transduction

occurs only with temperate phage, those thancan enter the host chromosome to act as an episome and creating a lysogenic strain. The phage is called a prophage when integrated. The viruses that do this are called "temperate"and when integrated into the host protect it from "attack" by the same virus. In a lysogenic strain, phage reproduction is prevented by expression of a gene that represses other virus genes from being expressed.

Fragile X Syndrome

occurs when a CGG repeat in the leader of the FRAXA gene and mRNA expand to over 50 copies

commaless

once translation begins, codons are read with no break

Sickle cell mutation

one T to A mutation, that causes glutamic acid to be replaced by valine

When does NPD occur in linked genes

only a four strand double cross over (DCO or DXO) gives a NPD; this will be very rare if the genes are close together.

Mosaics

only half of the cells are aberrant

Where does meiosis occur?

only in germline cells. It requires two divisions following one round of DNA replication

monofunctional glycosylase

only remove the base from the backbone and require a separate lyase to make a nick

Gap Genes

organize cells into groups of segments along anterior-posterior axis If gap genes are defective, the embryo will be missing some of the normal thoracic (T) or anterior (A) segments. All gap proteins are transcription factors.

pair rule genes

organize cells into individual segments These genes are expressed in alternate stripes, based on positive and negative interactions with the previously established gradient of transcription factors. (11-12 nuclear division stage)

OI

osteogenesis imperfecta

Dominant mutation example

osteogenesis imperfecti 1 X 10-5

Binomial Distribution

p is the probability of event x (a boy for example) and q is the probability of event y (a girl for example) (both would be ½ in this case) n is the total number of offspring, x is the number of one type and y of the other (can add Z if a third type, etc.)

gRNA

pair with bases in the target creating a template to direct the changes that can include adding, altering or removing bases.

Cellular level

papillae and tyloses

two types of inversions

paracentric, where the inversion is in one arm pericentric, where the centromere is included

What holds amino acids together?

peptide bonds

Examples of histone modifications that affect the binding of DNA to prevent or allow transcription

phosphorylation, typically of a serine (S) but sometimes Tyrosine (T); acetylation and methylation, most often of lysine (K)

Types of vectors

plasmids, viruses, YACs

PCR

polymerase chain reaction

allopolyploidy

polyploidy resulting from contribution of chromosomes from two or more species

PTGS

post transcriptional gene silencing

mRNA targeted for cleavage

post-transcriptional gene silencing (PTGS) RNAi

Alternative splicing in a-tropomysin

pre mRNA has 13 exons, 12 introns -Striated muscle; 10 exons included -Smooth muscle; 9 exons used; 7 shared

frameshift mutation in lac operon

prevent the synthesis and function of all subsequent enzymes

phosphatase

prevents ends of DNA from ligating

cotransformation

process in which two or more genes are transferred together during cell transformation

gene conversion

process of nonreciprocal genetic exchange that can produce abnormal ratios of gametes following meiosis In gene conversion, one allele present in meiotic pairs 'replaces' the other. This occurs at a higher frequency than can be explained by mutations.

snoRNA (small nucleolar RNA)

processing of rRNA

B cells

produce antibodies leukocytes

Folding of tRNA

produce the arms and anti-codon at the base

How DNA-dependent RNA polymerases know where to start

promoters

Chaperonins

protein molecules that assist the proper folding of other proteins

Apoenzyme

protein portion of an enzyme

transition mutation

purine to purine or pyrimidine to pyrimidine

Floxing a gene

putting a loxP on either end of a gene

Classical examples of quantitative trait model

rabbit ear length, number of rows of kernels on a cob, number of fingerprint ridges, red color in wheat kernels

generalized transduction

random bacterial DNA is packaged inside a phage and transferred to a recipient cell by means of lytic cycle

What can slow down translation?

rarely used codons

Type II restriction endonucleases

recognize and cleave within specific base sequences

Duffy blood group

red blood cell system useful for studying admixture between African and European derived populations

incomplete dominance example

red flower + white flower = pink flower

genetic heterogeneity

refers to cases where defects in multiple different genes can cause the same phenotype

compound heterozygote

refers to the fact that individuals may carry two different defective alleles; it often is not possible to predict the severity of symptoms in these cases.

multiple alleles

refers to the fact that there are many known mutations, each technically being a different allele

Phenocopy

refers to the situation where an environmental cause can mimic a gene defect. Phocomelia is a very rare recessive genetic defect in which the limb buds fail to develop. The child on the bottom has the mimic, in this case caused by exposure to thalidomide in utero.

Key terms

relative fitness or 'w' is typically defined in comparison to the most highly reproductive genotype, which is set at 1 the selection coefficient 's' describes the degree to which selection lowers the reproductive capacity of a genotype, that is, the fitness of the genotype becomes w = 1-s for a lethal gene or genotype, s=1 and w=0

However

relaxing selection does not lead to a rapid rise in the frequency of defective alleles; Hardy-Weinberg says they will stay the same unless something makes them change so we may now have just mutation left as an acting force if the cure, such as a special diet for PKU exists today, it will be available in the future

What happens after intron is spliced

remaining exons are then bound together

bifunctional glycosylase

remove base from backbone a makes a nick in the DNA

deletion

removes a nucleotide

oxidative deamination

removes an ammonia molecule directly from the amino acid

disadvantages of using BAC as a vector

repeated sequences included

Nitrous Acid (HN02) as a mutagen

replaces an amino group -NH2 with =O, and can cause mis-pairing.

chromatin remodeling complex (CRC)

reposition nucleosomes, allowing access to DNA-binding sites

lacI

repressor protein, binds to the operator of lac operon in the absence of lactose, preventing transcription from the second promoter.

Fitness and gene frequency

reproductive fitness may depend on gene frequencies

What binding of ubiquitin to proteins requires to occur

requires ATP and 3 proteins •E1, ubiquitin activating, E2 ubituitin conjugating, E3 ubituitin ligase

disadvantages of using cosmids as a vector

requires packaging

COLA1 and COLA2

responsible for collagen fiber production Made in pre and pro form rare amino acid sequence, mostly glycine (1/3)

I promoter

responsible for the transcription of the lacI gene which codes for a repressor protein. Very weak promoter and is transcribed rarely

segregational petites

result from a mutation in the nucleus. Genes such as cytochrome oxidase are coded in the nucleus, so if it is defective we would see a 1:1 segregation ratio. Here we have a petite crossed with a normal, and the diploid has mitochondria. If we allow these to segregate, then those who have the defective mitochondria due to the defective nuclear gene component will still be petite.

site of protein synthesis

ribosomes

Alternative splicing in Drosophila ADH gene

same enzyme from two different promoters -Larvae; mRNA derived from a 'near' promoter after 2 introns removed -Adult; distal promoter, extra intron removed from leader -Allows activation via a different set of trans acting factors

•When a cross between a line with the chromosome 9 markers: • Ds Wx Sh C1 -telomere in a maize line with no Ac crossed to a line with Ac (on a different chromosome) but homozygous for the recessive alleles wx; sh; c1, she noted that...

she noted that in the F1, a 'breakage-fusion-bridge' cycle was created. Each of the markers past the Ds where a break occurred showed the recessive phenotype. In the dividing endosperm cells, the broken ends often 'healed together', losing the end of the chromosome (and loss of expression of the dominant alleles) in the affected sectors. The healed broken ends would lead to a bridge between the poles in mitosis that would heal and break again. Those sectors of cells showed recessive phenotypes for all genes past the Ds breakpoint. Wx is waxy versus starchy as detected with iodine, sh/sh is shrunken, where normal sugar is not converted to starch and C1 is colored versus colorless.

Alu elements

short stretch of DNA originally characterized by the action of the restriction endonuclease

The meristematic region of onion root tips

shows cells at various stages of the cell cycle

Combinations of antibiotic resistance genes detected in E. coli

shows origins of E. coli samples containing drug resistance genes from human and poultry Up to 12 resistance genes in some of the 2,220 samples tested! resistance often increases in steps, which is the basis for the 'take all the pills, even after you feel better' directive that is typically given

Having extra copies of a gene added to plant genome can lead to...

silencing rather than increased levels of expression

Chiasma

site of crossing over

ATP dependent DNA binding complex

slide histones away or even remove them from a promoter region by using ATP allowing transcription to occur

siRNA vs. miRNA precision

small inhibiting siRNAs have very precise pairing/slicing with one target mRNA while miRNA s often have some mismatches with many mRNAs that include built in target sites and reduce translation more than slicing those messages

Concerns of genetic load

some are concerned that as we learn to treat genetic diseases such as PKU that used to be lethal, detrimental alleles will accumulate to the detriment of the population

How is it that selective genes are specifically methylated?

sort of a mystery fetal globin genes are produced in fetuses then that gene is methylated causing it to become inactive when adult globin needs to be made

DNA probing techniques

southern blots northern blots

What are internal transcribed spacers sometimes used for?

species identification

Diplonema

stage in prophase I of meiosis during which synaptonemal complex disassembles and homologous chromosomes begin to move apart

Quantitative Trait Loci (QTL)

stretches of DNA that either contain or are linked to genes influencing a trait such as behavior

DNA polymerase III

synthesizes new DNA only in the 5' to 3' direction

TET stands for

ten/eleven translocations

true-breeding

term used to describe organisms that produce offspring identical to themselves if allowed to self-pollinate

Guthrie test

tests for PKU

Ago2 (or other argonaute proteins)

that can bind the 3' ends of the fragments and help separate to single strands to deliver to the RISC

In animal cells, one of the first visible signs of entry to mitosis is...

the 'splitting' of the centrosome and subsequent migration of the centrioles to eventually form the spindle fibers and attachments to the kinetochores

Eugenetics

the attempt to improve the human species by selective breeding

Non-overlapping

the bases in a codon are used only in one codon

Genetic load

the burden imposed by the accumulation of deleterious mutations

Diakinesis

the chiasma begin to migrate to the telomeres

Crick reasoning for 3rd base degeneracy

the curve of the anticodon loop, leads to 'wobble'

As number of genes contributing to a phenotype increase...

the effects of each contributing allele diminishes and distinction between binomial classes becomes obscured. When the environment can also affect the trait it tends to become bell shaped (Normal Distribution).

monocot gametes and 'double fertilization'

the egg sac has 8 haploid nuclei, all derived from 1 by 3 mitotic divisions, 3 antipodal cells, 2 polar central cells, 2 synergids & 1 egg cell. The pollen haploid nucleus divides once to make a tube nucleus and a sperm nucleus which then divides again before fertilization.

Endproduct inhibition

the final product (E10) in a series of reactions inhibits an enzyme from an earlier step (E1) in the sequence In this example, histidine is the final product and acts as an inhibitor to the first enzyme in the metabolic pathway

pBR322

the first plasmid used in gene cloning Paul Berg shared 1980 Nobel prize in Chemistry for showing DNA could be sliced into a virus for transfer as well as developing a series of plasmid vectors

one gene-one enzyme hypothesis

the function of a gene is to dictate the production of a specific enzyme

Heritability

the genetic component of the variance measured for a trait

What happens if glucose and lactose are present?

the glucose is used before the lac operon is induced

Immunogenetics

the human immune system: acquired immunity via lymphocytes and antibodies doesn't develop until after birth

number of chromosomes is defined by...

the number of centromeres

Spermatogenesis

the production of sperm cells

Deamination

the removal of an amino group from an organism, particularly from an amino acid

ascus

the reproductive structure where spores develop on sac fungi

Any time the third base of a codon is a pyrimidine (U or C)

the same amino acid is coded

If the second base of codon is C, then...

the third base can be any base (often x is used)

lack of penetrance

the variability of expression may be so great that no symptoms are visible at all

DNA methylation in drosophila and yeast

there is no DNA methylation in Drosophila or yeast so it is not a universal mechanism.

Why can't bacteria express eukaryotic genes after shotgun cloning?

they have introns, different leader sequences, and are relatively large

quantitative traits

traits that show continuous variation (most traits, i.e.: height, intelligence, athleticism)

tRNA

transfer amino acids to the site of protein synthesis

Transduction in bacteria

transfer of DNA from a donor to a recipient bacterium by means of a virus vector

types of point mutations

transition and transversion

What kind of mutations do base analogs promote?

transitions

What kind of mutations do alkylating agents promote?

transitions and translations

How are most proteins made?

translation of mRNA

dsRNA viruses in plants

trigger a host response to destroy that RNA -Equivalent to RNAi that was later found in C. elegans and most other eukaryotes. -Has been developed into "VIGS"; virus induced gene silencing by replacing part of a virus with a sequence that will create a double stranded RNA by pairing with the targeted mRNA (based on antisense homology to the mRNA or via creating a hairpin structure that matches sequence from the mRNA)

What happens when poly-A tail is reduced to less than 60 A's in mRNA?

triggers 5' cap removal and rapid degradation

Where is TUT used?

trypanosome mitochondria and may help to explain their ability to overcome host defense

Hardy-Weinberg equilibrium

unless something forced gene frequencies to change, they should remain the same 'forever' in the population

Frequency of TT

up to 67%

bacterial transformation

uptake and incorporation of free DNA fragments into the host cell circular chromosome

Alkaptonuria

urine of an infected individual turns black when exposed to air showed typical single gene recessive inheritance

How Northern blots work

use a labeled DNA probe to detect complimentary RNA

Wu formula

used to calculate the probability that two genes will be co-transduced D is the 'distance' between two genes and L is the size of the fragment transferred.

Chemical oligonucleotide synthesis

used to make primers, adapters-linkers, promoters really inexpensive for short sequences

DNA oligomers

useful in making primers, linkers, promoters, signal sequences

Translation

uses the nucleotide sequence of a structural gene to make a chain of amino acids

Western blots

using a protein to detect another

how many repressor proteins per cell

usually around 10

VNTRs

variable number of tandem repeats

disadvantages of using YAC as a vector

very tricky to handle may combine different fragments and rearrange

When heterozygotes cannot be detected

we can only get an estimate of allele frequencies by making an assumption; that assumptions is called 'random mating'

polytene

when chromosomes replicate without cell division, so sister chromatids stay together in perfectly lateral register & are intimately synapsed

Pleiotropy

when multiple organs are involved; often seen as a syndrome

homodimer

when two polypeptides encoded by the same gene bind to each other to form a dimer.

intragenic mutation

where a second change restores at least some of the products' activity

intergenic mutation

where a second mutation allows a bypass of the first

RISC (RNA Induced Silencing Complex)

where complementary mRNA is 'sliced' by Ago2

migration

where migrants from a population with different frequencies assimilate into the population being examined, or where there is differential emigration of individuals carrying particular alleles

mutation

where one allele changes to the other

selection

where one allele or genotype is altered in reproductive capacity

This problem also demonstrates 'transgressive segregation',

where the extremes in the F2 go beyond the values of the original parents (both were 4' tall but the F2 range was 2'-6'). For transgressive segregation to occur, the parents must provide contributing alleles for different QTLs.

Neutral petites

where the mitochondria are defective and if you mix a haploid and they form a zygote, after meiosis they will all have functional mitochondria.

How dominant and recessive alleles are represented usually

with capital and lowercase letters sometimes represented by two letters

Tissue level

wound periderms and corky layers

The first proven mutagen

x-rays

YAC

yeast artificial chromosome

yeast/E. coli shuttle vectors

you start with E. coli genome with replication origin, amp resistant site, and polycloning site, and URA3+.

How to link amino acids

you take on O- from a carboxy and hook it to the amino by taking off H2, which releases H20 and forms a peptide bond

Spontaneous/Random mutation theory

§ Mutations are random events § Can occur in the presence or absence of mutagens

Math things to remember

• 6! = 6 X 5 X 4 X 3 X 2 X 1 • 6! also = 6 X 5! or 6 X 5 X 4! etc. • 0! = 1 by definition • (N)^0 = 1

Antigen/antibody interactions define ABO Blood types Discovered by Landsteiner (1901)

• A and/or B antigens are on the surface of red cells • persons make antibodies against A and/or B antigens they do not have* • blood mixed on slides from different individuals could identify 4 groups • A with A is OK, or B with B is OK • A with B or vice versa, agglutinate and would cause death if used in transfusion • O blood is OK with O, A, B, or AB as it does not have A or B antigens (but does have some anti A and anti B) O individuals have H antigen; it's a precursor to making A and B •AB cells agglutinate with antibodies* in blood from either A or B individuals

5-azacytidine

• Bind and inhibit DNA methyltransferase enzymes

Bee sex determination

• In bees, males (drones) are haploid from unfertilized eggs, workers are diploid and queens are diploids who have been fed royal jelly by workers. The queen controls which eggs are fertilized. The drones produce sperm by mitosis.

Neurospora sex determination

• In fungi such as Neurospora, either the 'A' or 'a' mating type allele strains develop female structures if placed on medium with low levels of NH3. The other mating type then serves as the male.

yeast sex determination

• In yeast, mating type switching can occur since both 'a' and 'alpha' cassettes are present; switches occur (or are detected) when all of one mating type are present.

Chemical resistance - induced Here are 'active defense responses' we will consider where the plant makes specific chemicals only after being exposed to a pathogen. Generally the responses are not pathogen specific and are also induced in some cases by stress or even by non pathogenic microbes.

• Phytoalexins - antimicrobial compounds produced de novo in response to challenge by a pathogen •Production of phytoalexin compound is more rapid and/or with greater accumulation in incompatible interactions than with compatible interactions •Virulent pathogens are typically less sensitive to phytoalexins produced by the host than are avirulent pathogens •Antifungal Enzymes and Defensins •Reactive Oxygen Species

Since inversions prevent recovery of recombinant gametes, genes within an inversion can be maintained as a block. Drosophila geneticists developed "Balanced Lethal" stocks for each chromosome involving nearly full length inversions.

• the C in the ClB strain that Muller used to show X-rays cause recessive lethals on the X chromosome was actually an inversion, it didn't suppress crossing over, just the recovery of XO gametes • another example is shown here; each marker is lethal when homozygous so the stock can be maintained by sib matings. Genes: (Cy is curly wing, L is lobed eye and Pm is plum) • these genes are on chromosome 2 and the stocks can be used to test for mutagens through breeding treated males and using a series of crosses to see if the treatment causes recessive lethal mutations.

Intraspecific crosses

•, crosses between Bos indicus (Asian cattle such as Brahman) and Bos taurus (European breeds such as angus) are fertile and cross breeding has been successful in creating new breeds with features of both. Both of these species have 60 chromosomes, so perhaps the species separation is in question.

Repeats in centromeric regions

•100's to thousands of short repeats in centromeric regions -CenP-B box and alphoid repeats are present from flies to humans

unambiguous

•A codon always calls for the same amino acid (with a few special exceptions)

The Hypersensitive Response (HR)

•A rapid, localized, necrotic host response •Characterized by accumulation of phytoalexins, oxidative burst, lignin accumulation, ion flux •Typically a highly specific host response, often due to a single resistance gene •Results from interaction of resistance gene product (host) with avirulence gene product (pathogen) to initiate a signal transduction pathway

Exceptions to universality

•AUA can sometimes be used as a start codon in many species •Some apparent 'exceptions' turned out to be cases where mRNA editing changes specific bases in a message before it is translated; this is most often seen in plant organelles, but important examples also occur in humans •UGA when surrounded by specific bases can be used to insert selenocysteine or pyrolysine. This requires the aid of a special tRNA and specific enzymes that alter the cys or lys before insertion.

Other Ac-Ds facts

•Ac is 4,583 base pairs long. •The transposase/integrase is only expressed in developing tissues and not in germline cells. •The typical rate of transposition is 1 in 10^5 to 1 in 10^7 per DNA replication •Other maize Tn systems include En-1/Spm and Mutator, which transposes more often, especially in developing gametophytes. •Combined with T-DNA of Agrobacterium tumefaciens to transfer.

Albinism

•Albinos are unable to make the pigment melanin Recessive inheritance

Law of Segregation

•Alleles assort to gametes in a random fashion. -That is plants with the genotypes AA or aa are homozygous and give only A or a alleles respectively, while heterozygous Aa plants produce ½ A gametes and ½ a gametes. -Random union of male and female gametes accounts for the 3:1 phenotypic and 1:2:1 genotypic ratios in the F2. •All the examples he reported show simple dominant and recessive alleles for each character, although he did indicate that for one trait, he felt the heterozygotes were intermediate. -(*some consider Dominance to be the first law, making this the second, while others say dominance is the third law or leave it out all together)

DNA Polymerase DNA repair

•Almost every DNA polymerase has a 3' to 5' exonuclease activity so that it can back up and remove a mismatched base (about 1 in 105 base mismatches form during replication in E. coli). The exonuclease activity helps lower the actual error rate to 1 in 107 to 1 in 1011.

components of translation

•Amino acids •tRNA •Ribosomes -rRNA -Many proteins •mRNA

effects of aneuploidy

•An extra or missing chromosome is generally extremely detrimental -We have seen a few exceptions in sex chromosomes (XXX, XO, XXY, XYY) -a missing autosome (2N-1) or monosomy in somatic cells is generally lethal •No human monosomics or nullisomics (missing one pair) can survive •In some plants that are 4N or 6N, one missing chromosome may be tolerated

What synthesizes RNA primers?

primase

core enzyme

prokaryotic RNA polymerase consisting of α, α, β, and β' but missing σ; this complex performs elongation

DNA gyrase

relaxes supercoiling ahead of the replication fork by breaking both strands and untwisting

DNA polymerase I

removes the RNA primer and replaces it with DNA

Forms of DNA

"A" form, "B" form (Watson and Crick), and "Z" form

Enhancers

A DNA sequence that recognizes certain transcription factors that can stimulate transcription of nearby genes.

Hydrogen bonding for purines

3 hydrogen bonds holding guanine and cytosine together; two hydrogen bonds linking oxygen and hydrogen, and one hydrogen bond linking hydrogen and nitrogen.

Rate of transcription in eukaryotes in seconds

40-80 nucleotides per second

Meselson-Stahl Experiment

Designed an experiment to test the hypothesis that DNA is semi-conservative. Grew E. coli for many generations in a solution that was highly enriched in N-15 (heavy nitrogen). Over many generations, the majority of nitrogen in the E. coli's DNA would be N-15. They then took the bacteria that with the N-15 in the DNA and starved it, and then reintroduced the bacteria into a solution enriched in N-14 (regular nitrogen) and let them start growing. They allowed enough time for the bacteria to replicate their DNA, and removed the bacteria from the solution and extracted the DNA. The DNA was then put into cesium-chloride gradient and centrifuged it. They saw at 0 generations that had a density of DNA that corresponded to all N-15 DNA. At 1.0 generations there is a lower density of N-15 DNA. At two generations, the density showed that all were all N-14 DNA, indicating that DNA replication is semi-conservative.

What did base pairing and the double helix hint at?

Base pairing hinted at how DNA replication works, because if you pull the template apart, then each strand could be used as a template strand to make a new strand.

Griffith (1928)

He had two forms of pneumococcus, a bacteria that would cause pneumonia in mice; smooth that had a polysaccharide shell (like an m&m) ,and rough that did not have the polysaccharide shell. If a heat killed smooth bacteria was injected into the mice, no infection was seen. If live rough bacteria was injected into the mice, no infection was seen. If live smooth bacteria was injected, the mouse would get pneumonia and die. If live rough and dead smooth was injected, then sometimes the mouse would be infected with pneumonia and die. They found in these mice, that there were live rough and smooth bacteria in the mouse.

problem with rapid transcription in prokaryotes

Since no nuclear membrane is present, translation can begin as soon as part of the message is available. If transcription gets too far ahead of translation, there is a long strand of unprotected mRNA which is very fragile.

Is there only one sigma factor?

No, there are different sigma factors that function with special motifs for special 'stress' situations.

Was the new smooth bacteria genetically identical to the killed smooth bacteria?

No, this is a mutated form of the rough bacteria, not the rebirth of the original smooth bacteria.

Components of nucleotides

One phosphate group, a 5-carbon sugar (ribose in RNA, deoxyribose in DNA), a nitrogenous base

Hershey and Chase (1952)

Proved that DNA carries genetic information in the T2 virus. Bacteria was grown in the presence radioisotope P-32 and since the bacteria would make all of the nucleotides the virus would then use to incorporate into its own DNA, this would give them some labeled virus and host labeled DNA. In another experimental batch, they grew the bacteria in medium that contained S-35 (radioactive sulfur). S-35 in only found in proteins, so this batch would only have proteins labeled. The virus would then infect the bacteria and the bacteria would be collected. Then, they would watch would happen when the virus reproduced inside of the bacteria. They then examined if the radioactive signal was coming from the outside of the cell or the inside. For the S-35 batch, radioactive signal was coming from outside the bacteria, indicating that the virus's protein was outside of the cell, and the radioactive protein was not found in the virus' progeny. For the P-35 batch, the radioactivity was inside the bacteria, indicated that the virus's DNA was transferred into the bacteria, and the radiactive DNA was found in the virus' progeny. Proved that DNA is the heritable material and not proteins.

What are primers made of?

RNA

How DNA synthesis occurs

Starts with the 5' base and adds new bases by removing a diphosphate from the next nucleotide and connecting the alpha phosphate to the last 3' OH.

Watson-Crick Model

They put the phosphate sugar backbone on the outside of molecule, like a spiral staircase, with the nucleotides extending into the middle of the molecule, like steps on the staircase.

Tobacco Mosaic Virus (TMV) experiment

This a virus that infects susceptible tobacco plants. TMV only has two molecules, an RNA core and a coat of lots of copies of a code protein. Two TMV were combined, TMV type B and TMV type A. The RNA core of TMV type A was used and was coated with the proteins from TMV type B. When the newly formed virus infected a leaf and replicated, the progeny had RNA and proteins from TMV A. This proves that the nucleotides in RNA coded for the proteins in the progeny, and not the other way around.

Types of snRNPs

U1, U2, etc.

What did Wesiman describe and when did he do it?

Weisman observed meiosis in 1890, but also noted the role in making haploid gametes, so he is often credited as the discoverer of mitosis

Initial problems with the Hershey-Chase experiment

When they tried to collect the bacteria after the infection, they found that the bacteria had both S-35 and P-32 labels. This was partly because the viruses with the S-35 labeled proteins on the newly infected bacteria were stuck to the outer membrane. So, if they put in a waring blender for a while that would get rid of the viruses stuck to the membrane.

U1

binds to 5' splice site

shape of DNA in prokaryotes

circular

What are chromosomes of higher organisms made of?

composed of two components: DNA (nucleic acids) and proteins

sigma factor

controls the binding of RNA polymerase to the promoter (TATA box)

Where are proteins stored in a eukaryotic cell?

cytoplasm

DNA dependent RNA polymerase

enzyme that uses DNA as a model to build the mRNA chain

How do we read nucleotides?

from 5' to 3'

How are nucleotides held together to form a double helix

hydrogen bonding

semi-conservative

in each new DNA double helix, one strand is from the original molecule, and one strand is new

Protection of mRNA

mRNA must be moved from the nucleus to the cytoplasm. To protect the mRNA, when the message is being synthesized a 5' cap is placed at the beginning of the message, and a poly-A tail is added is added which can consist of 100's of A's.

nucleoside vs nucleotide

nucleoside: sugar + base nucleotide: sugar + base + phosphate

What are nucleotides held together by in a polymer

phosphodiester linkage

pre-mRNA

precursor mRNA; the first strand of mRNA produced by gene transcription that contains both introns and exons

Silencers

repressor proteins that may bind to DNA sequences and inhibit the start of transcription

How does DNA polymerase start?

require a 'primer' to get started

Prokaryotic promoters

the same for making mRNA, rRNA and tRNA and they have 1 RNA polymerase

Transcription

uses DNA as a template to make RNA