Main characteristics of x-linked dominant pedigrees

• trait is common in pedigree
• all male affecteds pass trait to their daughters
• male and female have an equal chance at being affected

Characteristics of x-linked recessive inheritance

• trait is more common in males than females
• affected man passes gene to all daughters
• a son of carrier mother has 50% chance at inheriting the trait
• male to male transmission never occurs
• carrier females are usually asymptomatic
• trait is rare in pedigree
• trait skips generations

what is cystic fibrosis

affects lungs, increased mucus, average lifespan: 31 years

most common autosomal recessive gene in europeans

heterozygotes may have or had selective advantage due to cholera, typhoid, or other diseases

affecteds have two inactive copies of CFTR (cystic fibrosis transmembrance conductance regulator) gene

the delta508 mutation results in 3 bp deletion and a nonfunctional protein

characteristics of y-linkage (plus example)

affects only males

all sons of affected males are affected

ex. hairy ear rims

Describe Caenorhabditis elegens

Nematode (round worm), Hermaphrodites & Males

Natural Habitat: Rotting Fruit & Soil

Length: 1 mm (Adult)

Food: OP50 E. coli

Cellular Structure: ~1000 eukaryotic cells; ~300 neurons

Genome Sequenced:

Classical Forward/Reverse Genetics

RNAi by Feeding (Phenotype Analysis Next week)

Phenotype Analysis of Genetic Mutants

what microscopes are used to observe c.elegens and for what?

Stereomicroscope:

• Growth&Development
• Behavior (i.e. feeding,movement,etc.)
• Reproduction

Compound Microscope:

• Tissue Structure
• Cell Structure
• Organelles
• Protein Expression

what are the developmental times for c.elegens

14-16 hours for egg to hatch

3 days from embryo to egg laying

who researched c.elegens and when did they earn nobel prizes?

Sydney Brenner, john Sulston, bob Horvitz (received Nobel prize 2002)

andy fire, craig mellow (nobel prize 2006)

martin chalfie (nobel prize 2008)

what two sexes are c.elegens

hermaphroditic and male

What is this mutant?

uncoordinate (unc)

What is this mutant?

Roller (rol)

What is this mutant?

Dumpy (dpy)

What is this mutant?

Blister (bli)

Define forward genetic screening

Isolation of mutants that show differences in phenotype for the process of interest, then find the associated genes

Define reverse genetic screening

Start with the analysis of a specific gene and then study the phenotype associated with it when mutated or subjected to RNA interference

What are the steps of forward genetic screening?

1) Determine biological process of interest to study

2) Produce mutagenized population of animal

3) Screen for phenotype of interest (based on biological question of interest)

4) Analyze mutant with specific phenotype

5) Map gene of interest

6) Conduct more screens to identify pathways or other genes involved with process

Define a mutagen

A mutagen is a chemical or physical agent that directly or indirectly causes DNA mutations

What does ethylmethane sulfonate do?

altars guanine leading to abnormal base pairing with thymine (from G-C to G-T)

what is RNAi

is a method to study gene function by reducing expression (silence) of a specific gene of interest

What are important findings from RNAi studies?

dsRNA in eukaryotic cells are perceived as a sequence-specific signal to inhibit expression of the corresponding mRNA. Various proteins are involved with the processing of RNAi.

Major findings:

• A few molecules of dsRNA can direct the destruction of much larger amount of mRNA
• Transmission of RNAi is across generations
• RNAi can be used as a tool to reduce expression of specific genes
• Universality of RNAi in eukaryotes
• RNAi mechanisms are a great genetic tool – but probably exists for a BIOLOGICAL purpose.

What are the general steps of RNAi?

1.Dicer family of proteins process dsRNA to initiate gene silencing generating small interfering (si)RNAs of ~21 nucleotides.

2.(si)RNAs target endogenous mRNA (specific for gene of interest). (si)RNAs guide sequence specific silencing RISC complex.

3.The mRNA is cleaved, thus not translated and protein product not made.

Explain the process of worm picking and general c.elegens husbandry

How to pick worms

1.Flame the tip of your pick briefly to sterilize it

2.Let it cool for 1-2 seconds

3.Scoop up some “sticky” OP50 bacteria by touching it to the edge of a thick bacterial lawn - this is your “glue”.

4.Hold your pick underneath the microscope (look through with both eyes). Rest your hand against something solid to stabilize it.

5.Touch the bacteria on the end of your pick GENTLY to the top of a worm - the worm should stick to the glob of bacteria .

6. Move to a fresh plate, make sure that the lawn on this plate is in focus, and gently touch the worm to the surface of the new plate. If the worm does not swim off the pick, slowly (and very gently) drag the pick across the surface of the plate. Do not break the surface of the agar plate with your pick

General husbandry

• Worm Pick
• Glass tubing and platinum wire
• NGM Plates – Nematode Growth Media
• Easy to contaminate
• Wear gloves
• Don’t touch media
• Work close to the flame
• Keep lids on when not picking
• Flame platinum wire each time
• E. coli lawn – OP50 Strain

What is population genetics

study of genetic variation within a population.

Combines Darwinian selection and Mendelian inheritance

Define population

a localized group of individuals of the same species.

define species

a group of populations whose individuals have the ability to breed and produce fertile offspring

What is a populations gene pool?

A population’s gene pool is the total of all genes in the population at any one time.

What are the important things about the hardy-weinberg theorem

Used to describe a non-evolving population.

Shuffling of alleles by meiosis and random fertilization have no effect on the overall gene pool.

Natural populations are not expected to actually be in Hardy-Weinberg equilibrium.

Deviation from H-W equilibrium usually results in evolution.

What are the assumptions of the H-W theorem

–Large population size: small populations can have chance fluctuations in allele frequencies (e.g., fire, storm).

–No migration: immigrants can change the frequency of an allele by bringing in new alleles to a population.

–No net mutations: if alleles change from one to another, this will change the frequency of those alleles.

–Random mating: if certain traits are more desirable, then individuals with those traits will be selected and this will not allow for random mixing of alleles.

No natural selection: if some individuals survive and reproduce at a higher rate than others, then their offspring will carry those genes and the frequency will change for the next generation

What is the hardy-weinberg theorem and equation?

The gene pool of a non-evolving population remains constant over multiple generations; i.e., the allele frequency does not change over generations of time

1.0 = p2 + 2pq + q2

where p 2 = frequency of AA genotype; 2pq = frequency of Aa plus aA genotype; q 2 = frequency of aa genotype

What is microevolution?

Evolution within a species/population = microevolution.

Microevolution refers to changes in allele frequencies in a gene pool from generation to generation. Represents a gradual change in a population

What are the causes of microevolution?

1)Genetic drift

2)Natural selection (1 & 2 are most important)

3)Gene flow

4)Mutation

Genetic drift definition?

the alteration of the gene pool of a small population due to chance

2 causes of genetic drift:

Bottleneck effect may lead to reduced genetic variability following some large disturbance that removes a large portion of the population. The surviving population often does not represent the allele frequency in the original population.

Founder effect may lead to reduced variability when a few individuals from a large population colonize an isolated habitat.

What is gene flow

is genetic exchange due to the migration of fertile individuals or gametes between populations

Important info about the cell cycle

• Tightly controlled
• Cellular checkpoints preventing cells from dividing when they should not.
• Mutations in a cell’s DNA change the timing of signals that tell when to grow and divide.
• Abnormal growth of cells results in a group of disease called cancer.

Define oncogenes and tumor suppressor proteins

Oncogenes- DNA that codes proteins that promote normal cell growth and division. Mutations can cause these genes to become active at the wrong time or place.

Tumor Suppressor Genes- DNA encoding these proteins inhibit cell growth and prevent tumor formation.

Define somatic mutations and germline mutations

Acquired (somatic) mutations: Exposure to mutagens that affect the DNA; Errors during replication.

Germline mutations: Directly inherited through generations.

What is P53

p53, tumor suppressor protein:

• Gene located on the short arm of chromosome 17.
• Mutations to the gene causes the protein to loses its ability to bind to DNA.
• p53 that have mutations in specific hot spots promote uncontrolled cell growth and therefore function as oncogenes.

For p53 to play a role in cancer, both alleles need to be altered.

Information on Karyotyping

Chromosomes are generally classified using multiple criteria. They are matched and numbered from largest to smallest, G-banding, and centromere location

What is sickle cell disease

• Is an inherited blood disorder that affects around 5 million people worldwide.
• The disease is caused by small changes in an individual’s genetic coding that interfere with their body’s ability to create hemoglobin- a protein that transports oxygen. Individuals with SCD have red blood cells that are misshaped, stiff, sticky and short-lived.
• These individuals often have anemia- a medical condition characterized by low red blood cell numbers and low blood oxygen levels.
• Many people with SCD also experience periodic blood clots, that block the flow of oxygen to other important organs, and have compromised spleens.
• These conditions result in number of symptoms ranging from chronic tiredness to heart attacks.

What chromosome is the beta-globin gene found on?

chromosome 11

What does CRISPR stand for and briefly (kinda) explain how it works

• CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats .Some bacterial species use these genetic information as part of an antiviral system.
• When a virus invades a bacterial cell, the bacterium identifies the virus as foreign and collects some of its DNA so that it can be recognized the next time it shows up.
• The bacterium puts the viral DNA into a spacer in the CRISPR section of its own DNA. As the spacers fill up, they become a database of viral enemies.
• The spacers (viral DNAs) are combined with Cas (CRISPR-associated enzymes), which are always found next to CRISPR sequences. Together, the spacer sequence and the Cas protein can effectively serve as a bacteria’s immune system.
• To set up an ongoing defense system, the bacterium takes each piece of viral DNA out of storage in the spacers and transcribes it into a strand of RNA.
• This strand of RNA is known as the guide RNA (gRNA). Cas enzyme then binds to the gRNA, “loading” the Cas protein.
• Together, gRNA-Cas (commonly referred to as CRISPR-Cas) drift through the cell. If they encounter foreign DNA that matches the spacer sequence, the gRNA will base-pair to it, and the Cas enzyme will chop the invader’s genome into pieces which prevents the virus from replicating.
• The system only cuts DNA that’s specific to the RNA spacer sequence. Therefore, CRISPR-Cas allows bacteria to find any short sequence of DNA and attack it with precision.

Explain round vs. wrinkled kernels for corn genetics

Round: starchy, contains small amount of water; when dried, stays round

Wrinkled: sweet, contains a significant amount of water; when dried, wrinkles

What colors purple corn purple and why is some corn yellow

• Kernels have a purple color because the aleurone is colored by purple pigment, anthocyanin, which hides the yellow color of endosperm (and a skin, which covers a kernel, is thin).

Kernels have a yellow color because the aleurone is colorless due to synthesis of defective enzyme for pigment manufacture and kernels will have the color of endosperm that is yellow

Briefly explain enzyme site digestion

Each enzyme digests (cuts) DNA at a specific sequence = restriction site

Briefly explain gel electrophoresis

DNA fragments are loaded into an agarose gel slab, which is placed into a chamber filled with a conductive buffer solution.

A direct current is passed between wire electrodes at each end of the chamber. Since DNA fragments are negatively charged, they will be drawn toward the positive pole (anode) when placed in an electric field.

Smaller DNA fragments can move more easily than larger ones. The rate at which a DNA fragment migrates through the gel is inversely proportional to its size in base pairs.

Bands will be seen in the gel after the DNA is stained.