learning objectives

complementation tests

complementation tests

1. If you have 2 mutants w the same phenotype you want to know if that’s because of the same gene

   1. same gene: will still have mutation

   2. different genes that do the same thing: will be wild-type

2. Most mutations are recessive, because most of the time, one copy of a gene that functions properly is sufficient to produce enough functional protein. Most mutations cause defects in gene function.

3. Cross two mutants with the same recessive phenotype and see if the offspring have the phenotype as well.

   1. You have isolated two independent mutant fruit flies that have white eyes when they are homozygous: are they different mutant alleles of the same gene?

   2. Cross mutant 1 to mutant 2

DNA

proven necessary and sufficient for transmitting genetic information via:

• Avery showed that mutant bacteria can be transformed via exposure to extract from wild type bacteria (positive control). in the transformation they take up heritable instructions. if the extract is exposed to dnase, the experiment no longer works. therefore dna is necessary. treatment of the extract with any other kind of enzyme had no effect (negative control).

• in the lab, we transformed bacteria with pure dna in calcium chloride solution. therefore dna is sufficient. bacteria exposed only to calcium chloride solution were not transformed (negative control). the untransformed bacteria could grow in the absence of antibiotic (positive control) but not in the presence of antibiotic (negative control).

genetic code

“cracked” by:

1. Genetic mapping of mutants within a bacteriophage gene showed that the colinearity of amino acids and proteins: mutations that mapped near each other affected nearby amino acids!

2. Mutations disrupt the amino acid sequence in proteins

3. Genes must encode proteins’ amino acid sequences

4. Adjacent codons in DNA determine adjacent adjacent amino acids in proteins.

eukaryotic gene

• oriented so that the sense strand has its 5’ end on the left and its 3’ on the right. boxes are exons and the lines between them are introns. the line 5’ to the first exon is the location of the promoter. the first exon has a black portion before the first codon. that is the 5’ utr. the last exon has a gray portion after the stop codon. that is the 3’ utr. the promoter (along with other regulatory information in the introns and far 5’ and far 3’ to the portion shown here) determines how efficiently the gene is transcribed into mrna (and in what tissues and at what times).

• the 5’ utr contains information that determines how efficiently the RNA for this gene can be translated into protein. the yellow portions of the gene are the coding regions of the exon. that is what determines what amino acids are added in what order, which determines the protein structure and function. the 3’ utr contains information that controls efficiency of translation, mRNA stability, and mRNA localization in the cell.

transcription

DNA breaks into 2 separate strands and is transcribed by mRNA

translation

in the ribosome, mRNA provides codons to decode the bases and synthesize proteins (tRNA)

mutations

effects on different gene regions include:

1. Coding regions: __ in coding regions can lead to changes in the amino acid sequence of proteins, potentially altering protein function or structure, which can affect the phenotype.

2. Regulatory regions: __ in regulatory regions, such as promoters or enhancers, can impact gene expression by affecting the binding of transcription factors or RNA polymerase, leading to changes in the amount of mRNA produced and ultimately influencing protein levels and phenotypic outcomes.

transcription factor

regulates eukaryotic and prokaryotic genes by:

• one part of the __ reaches into the DNA and “reads” the bases: the protein can only stick to certain DNA sequences. Another part of the transcription factor binds to other proteins (e.g. To proteins associated with RNA polymerase, or to chromatin modifying enzymes).

signaling pathways

1. Pathways in which each step modifies a product produced in the step before (substrate-dependent pathways)

2. Pathways whose activity can be “on” or “off.” In these pathways, mutants have one of two opposite phenotypes, and can bypass the need for upstream genes (“switch” pathways).

genetic engineering

1. Modify the germ cells to generate transgenic offspring

2. Modify a patient’s stem cells in the lab and reintroduce them

3. Infect the patient with a virus that will genetically modify specific populations of cells in the body.

Important uses eg. SCID patients, extract bone marrow cells → add a wild-type copy to the effected gene → return cells to patient’s bone marrow

cancer

a disease of genetics and development characterized by

• Independence from external and internal growth signals

• Defects in apoptosis (programmed cell death)

• Continue to divide indefinitely

• Genetically unstable

1. Can be caused by: mutations (usually more than 5)

   1. eg. uncontrolled division can be caused by gain-of-function of genes that encourage growth (“proto oncogenes”) or by loss-of-function of genes that discourage growth (“tumor suppressors”).

   2. Mutations in genes that regulate tissue invasion, cell death, and many other pathways are mutated in most __ cells.

   3. One early step in most __ is to lose function in DNA repair pathways. This causes genome instability (mutations).

2. Can be treated by:

   1. Surgery: Remove tumor before metastasis (if accessible). Ensure healthy tissue removed on all sides.

   2. Radiation: ancer cells divide quickly, often don’t stop to repair damage → more sensitive to radiation

   3. Chemotherapy: base analogs and base modifiers can cause unrepaired mismatches in cancershis can kill cells

      • Hormone antagonists can shrink hormone-dependent tumors

      • Drugs can target growth pathways that help cancer cells grow

   4. Unfortunately, some cancer cells lie dormant and resist radiation and chemotherapy treatments. Cancer cells can also adapt, evolving to be less reliant on a pathways that are under attack.

unequal cell division

division of a cell into daughter cells with unequal sizes or contents

• can occur due to various factors eg. uneven distribution of cellular components during mitosis or meiosis, unequal distribution of organelles, or unequal partitioning of cytoplasmic contents.

cell fate determination

what kind of cell a cell will develop into

• can be determined by which feedback loops they utilize (ie. positive v. negative)

cell migration

cells move from one place to another in the body, guided by signals and cues. It's essential for processes like wound healing, immune response, and development.

cell proliferation control

like a traffic signal for cells, regulating how quickly they multiply. It ensures the right balance between growth and stopping to prevent overcrowding or runaway growth, which could lead to problems like cancer.

human development

important events:

1. fertilization

2. nuclear fission, cleavage, compaction

3. implantation

4. primitive groove formation

5. sry + gonad development

6. quickening

7. viability

8. birth

reproductive human cloning

process:

1. To do __ on an adult, remove the nucleus from a donor egg and replace it with the nucleus of a cell from the person you want to clone. Activate the egg to induce development. At the blastocyst stage, implant the embryo in a surrogate’s uterus.

2. Identical twins are clones of each other.

therapeutic human cloning

process:

1. Remove the nucleus from an egg and replace it with the nucleus of any somatic cell from the patient. The egg now has two copies of every gene.

2. Scientists “activate” the egg to induce embryonic development. The embryo is harvested to produce ES cells that are genetically identical to the patient. These cells can be used to produce cells and tissues the patient needs.

iPS cell technology

induced pluripotent stem cells (de-differentiated), generated by inducing expression of many different combinations of genes and starting with many different cell types

ES cell technology

ES cells can be genetically engineered via adding DNA to them or by altering their DNA sequences

germline genetic engineering

treatment not just for the patient, but all future generations

1. Method 1: genetically modify a germ cell or fertilized egg

2. Method 2: modify ES cells and create a chimera that is comprised of modified-genome cells

somatic cell genetic engineering

editing the genes of a living differentiated cell (can be done via CRISPR)

hardy weinberg law

if certain criteria are met, the frequency of alleles in a population will not change (i.e. there will be no evolution). In one generation, populations would assort into stable genotypic and phenotypic frequencies:

1. Let p = frequency of A allele

2. Let q = frequency of a allele

3. If these are the only two alleles, p + q = 1

4. % AA = p2        % Aa = 2pq       % aa = q2

evolution

the accumulation of changes in the genes of populations over time; the change in allele frequencies in a population over time

• eg. english moths

natural selection

• acts on individuals; the fitness of an individual/ability to successfully reproduce; living things appear very different today because of heredity and competition

• occurs in nature because of limited resources—not every individual can breed, and genetic traits are one factor in determining breeding success

• detected via: Endler

  • Prepared artificial streams with black, white green, blue, red, and yellow gravel.

  • He bred guppies from various regions to generate an incredibly heterogeneous pool of guppies with different spots. He then let them grow for several months in the various artificial streams. Then he added some natural predators.

  • Prediction—over time, guppies will evolve to have spots that match the gravel in their stream. Streams with more dangerous predators will lead to even closer matches than streams with less dangerous predators.

  • After 10 generations:  streams with no predators yielded extremely colorful guppies with big spots. Guppies contrasted highly with gravel color.

  • Streams with dangerous predators yielded guppies with small, dull spots. Guppies blended in with gravel color.

genetic drift

• permits a population’s allele frequencies to change (evolution) even when the allele increasing in frequency does not affect fitness

altruism

when one individual helps another, even at some personal cost

• In general, alleles that increase an individual’s fitness are transmitted more efficiently to the next generation

sexual reproduction

generally includes meiosis: the maternal and paternal chromosomes exchange genetic information. Then the recombined chromosomes are placed in different eggs or sperm. 

sexual selection

selection often unrelated to fitness

• We see many traits in nature that seem to reduce fitness

  • eg. brightly colored birds, male-male combat

• Fitness is defined not as health but as reproductive success

  1. You have to survive to reproduce

  2. You have to find a mate (and a good one!)

• Sometimes survival and competition for mates are in conflict and a compromise is reached.

senescence

aging

• Natural selection becomes less powerful as organisms grow older and more of their reproduction is done.

• There is a trade-off between early fitness and late fitness and between reproduction and health (e.g. allocating resources to reproduction versus repair).

deep sea vents

potential origin of life on earth

• High pressures and steep temperature gradients near __ could have permitted accumulations of complex molecules where they would have also been protected from cosmic radiation.

• At __, H2 and CO2 are often available for chemical conversion to CH4 (methane) and water. This releases energy and provides building blocks for life. This is also how many bacteria still make a living.

natural selection

experiments testing predictions of it include Darwin

race

not a genetic category because:

1. Most human genetic diversity is within ___ or present in several different __

2. A lot of human genetic diversity is specific to very small populations

3. Human genetic diversity is a subset of African genetic diversity (all other “__” are a subset of African people)

mutation

a change in a DNA sequence caused by errors during DNA replication or mutagens like radiation

• can be detected by DNA sequencing

• eg. substitutions, deletions, duplications, and insertions

• creates new alleles

Ras

a protein downstream of growth factor receptors that is activated when a growth factor binds to a growth factor receptor

• signals cell growth/survival/destruction

• can turn itself off so that its signal does not lead to a permanent response

events

major __ in human evolution include:

• LUCA