Genetics

What is mutation rate?

The number of events that produce mutated alleles per locus per generation.If 4 of 100,000 births show a mutation from a recessive to a dominant allele, we've ctually sampled 200,000 genes because we have two copies of each gene. So the mutation rate would be 4/200,000 or 2/100,000.

To ensure that the mutant phenotype can be measured, it must:

Never be produced by recessie allelesAlways be fully expressed and completely penetrant so that mutant individuals can be indentifiedHave clearly established paternityNever be produced by nongeneric agents such as drus or infection and be produced by a dominantly inherited mutation of only one gene

Mueller's Research

Focused on environmental causes of mutations

Ames and his test

Identified mutagenic agents but the disadvantage to this test was that he used bacteria, which is a different metabolic pathway than is found in rats or humans. Sonce the bacteria doesn't have that metabolic product, just abecause a chemical passes the Ames test, doesn't necessarily mean that it is not a mutanogen

Missense Mutations

Mutations that cause the substitution of one amino acied for another in a protein.Ex:CTC-->CAC (glutamic acid-->valine) (sickle cell anemia)

Sense Mutations

Mutations that change a termination codon into one that codes for an amino acid. Such mutations produce elongated protiens.Ex.UAA-->AAA (removal of termination codon

Nonsense mutations

Mutations that change an amino acid specifying a codon to one of the three termination codons. This shortens the protein product.Ex.AAA-->UAA (termination codon)

Frameshift Mutation

Mutational events in which a number of bases (other than multiples of three) are added to or removed from DNA, causing a shift in the codon reading frame.Insertion: CAT CAT CAT GCA TDeletion: CAT CAT CAC AT

Trinucleotide Repeats

A form of mutation associated with the expansion in copy number of a nucleotide triplet in or near a gene

How many trinucleotide repeats are there in Fragile X syndrome?

CGC - 230

How many trinucleotide repeats are there in Myotonic Dystrophy?

CTG - 50 to 2,000 repeats

How many trinucleotide repeats are there in Huntington's Disease?

CAG - 42 to 100

Anticipation

Onset of a generic disorder at earlier ages and with increasing severity in successive generations

Examples of DNA repair genes

UV damage - thymine dimers (excision repair)Xeroderma Pigmentosum - thymine dimer defectBloom Syndrome - DNA ligase defect

Genomic Imprinting: Reversible alterations to the genome

Activate certain genes and deactivate other genes. Sometimes, genes that are not necessary are activated and start influencing changes. This results in chance for mutations and an increase in the chance for cancer.

Teratogens

Fetal tissue mutations

Totipotent

A cell when it has the ability to give rise to an entire organism. Occurs during the 16 cell stage.

Clones

Genetically identical molecules, cells, or organisms all derived from a single ancestor.

Reproductive cloning and therapeutic cloning

The two types of stem cell cloning

Why stem cell clones are not exact replicas

1. telomeres of chromosomes of donor nuclei are shorter2. genomic imprinting when chromosomes are passed via germ line3. somatic cells accumulate mutations4. X-inactivation pattern 5. mitochondria is from recipient cell not donor cell6. coat color differences-pigmented cells move about differently7. environmental factors during embryonic/fetal development: nutrition (methylation) stress, exposure to environmental diseases

Why stem cell cloning fails

1. Meiosis not involved (meiosis in the female completes fertilization)2. Diploid nucleus is plunked into oocyte cytoplasm where signals direct it to do what a female secondary oocyte tends to do (a.) shed half of chromosomes as polar body--hapoid--lethal and (b.) replicates DNA--tetraploid--lethal

Bioethical issues of stem cell cloning

1. Violation of rights of early-stage embryos versus violation of rights of individuals who might benefit from such therapy2. 2001 USA legislation outlaw creating or selling "any embryo produced by human cloning

Steps of cloning genes

1. isolate plasmid DNA and human DNA2. cut both DNA's with the same restriction endonuclease--resulting in DNA fragments3. combine both DNA's--cut ends re-associate or anneal4. seal gaps with DNA ligase5. creates recombinant DNA molecules composed of human DNA and vector DNA6. transfer vector into bacteria 7. at each bacterial cell division, the plasmid is replicated resulting in many copies or clones of the DNA insert 8. lyse bacteria--extract recombinant plasmids9. cloned human DNA can be released from plasmid with same restriction enzyme used for cloning10. cloned DNA can be used directly, put in expression vector and transfected into cells

Human genomic library

1. A collection of clones that contain all of the genetic information in an individual--cut all DNA of donor cell--put in cloning vector (bacteriophage as an example)2. Retrieve gene of interest ("needle in hay stack") by using DNA probe3. DNA probe--a synthetic piece of labeled DNA that is complementary to part of gene of interest

cDNA library

Extract mRNA from cells, reverse transcribe to single stranded cDNA. DNA polymerase to give double-stranded cDNA, cut, put in cloning vector

Polymerase Chain Reaction (PCR)--1986

A method for amplifying DNA segments using cycles of denaturation, annealing to primers, and DNA-polymerase-directed DNA synthesis.1. DNA amplified by heating to break hydrogen bonds, yielding single strnded DNA2. Short nucleotide sequences act as primers for DNA replication added3. Enzyme, DNA polymerase, begins t primers and synthesizes a DNA strand complementary to the region between the primers, a proces called "primer extension"Ex.10 cycles = 1,024 copies 30 cycles = 1,073,741,820 copies

Southern Blotting

A method for transferring DNA fragments from a gel to a membrane filter, developed by Edwin Souther for use in hybridization experimentsUsed to find diferences in notmal and mutant alleles, identify related genes in other organisms, and study gene evolution

Western Blotting

Used for identifying proteinsUses same process in Southern Blotting only for proteins

Northern Blotting

Used for identifying RNADon't have to digest enzymes to study RNA like you would in Southern blots to study DNA

Recombinant DNA

A series of techniques in which DNA fragments are linked to self-replicating vectors to create recombinant DNA molecules, which are replicated in a host cell.Used in agriculture to make transgenic corn plants that are resistant to insects and to give transgenic pigs growth hormonesUsed in medicine and pharmacology to make human insulin via bacteria or milk from cows, goats, or sheepUsed in cloning pigs for organ donors (knockout of carbohydrate that is involved in transplant rejection)

Restriction enzymes

Bacterial enzymes that cut DNA at specific sites

Vectors

Self-replicating DNA molecules that are used to transfer foreign DNA segments between host cells

Transgenic

Refers to the transfer of genes between species by recombinant DNA technology; transgenic organisms have received such a gene

Applications of DNA technology

RFLP (restriction fragment length polymorphism)Prenatal (as well as postnatal screening for genetic defects)Paternity

Minisatellite

Nucleotide sequences 14 to 100 base pairs long organized into clusters of varying lengths; used in the construction of DNA fingerprints.

Short tandem repeat (STR)

Short nucleotide sequences 2 to 9 base pairs long otganized into clusters of varying lengths; used in the construction of DNA profiles

DNA profile

The pattern of of STR allele frequencies used to identify individuals

Cancer

Altered self cells that excape normal growth regulatory controls

1 in 3 will develop cancer in a lifetime

1 in 3 wil develop cancer in a lifetime

1 in 8 women develop breast cancer if the live to be 80

1 in 8 women develop breast cancer if they live to be 80

90% of lung cancer due to tobacco

90% of lung cancer due to tobacco

Stages in cancer

1. Initiation2. Promotion3. Progression/metastasis

Initiation stage of cancer

Event that is associated with the first mutation that leads to cancer

Promotion phase of cancer

Altered genes/cells increasing and recruiting mor growth factors, increasing the cells affected by the cancer.Benign or malignant can be determined at this point

Progression/metastasis stage of cancer

If tumor is malignant, the cells can spread to other parts of the body

Properties of Cancer

1. Clonally derived2. Accumulate mutations: display growth regulatory changes3. Movement-metastases4. Altered biochemical pathways5. Disorganized cytoskeleton6. Chromosomal abnormalities

Malignant transformation

1. Chemical--tobacco tar and SENCAR mice2. Virus--(Rous Sacroma virus (Peyton Rous); ERB-B (Bishop and Varmus)3. Translocation--Burkett's lymphoma (c-myc on chromosome #8 is translocated to Ig region on chromosome #14)

Causes of Cancer

1. Environment--lung and skin cancer2. Diet--fat: breast, prostate3. Chemical4. DNA and RNA viruses5. Genetics (approximately 10% of cancers)

Tumor suppressor genes

Genes encoding proteins that suppress cell division

Proto-oncogenes

Genes that initiate or maintain cell diveision and that may become cancer genes (oncogenes) by mutations

Oncogenes

Genes that induce or continue uncontrolled cell proliferation

Gatekeeper genes

Genes that regulate cell growth and passage through the cell cycle, for example, tumor suppressor genes

Caretaker genes

Genes that help maintain the integrity of the genome, for example, DNA repair genes

TREG cells

How to enhance immune response to cancer antigens/immunogens

Pathogens

Disease-causing agents

Antigens (antibody generators)

Molecules carried or produced by microorganisms that initiate antibody productionAny molecule that can bind to a antibody.Elicits celular and humoral response

Anitbody

A class of proteins produced by B cells that bind to foreign molecules (antigens)and inactivate them.Made in response to immunogen according to the specificity of the immunogen.

Immune System Branches

1. Humoral2. Cellular

Humoral Branch of Immune System

B cells/plasma cells make and secrete antibody/immunoglobulins

Cellular Branch of Immune System

T helpers enhance immune response; cytotoxic T cells destroy altered self

B cells

A type of lymphocyte that matures in the bone marrow and mediates antibody-directed immunity

Lymphocyte

White blood cells that originate in bone marrow and mediate the immune response

T Cell

A type of lymphocyte that undergoes maturation in the thyus and mediates cellular immunity

Helper T cell

A lymphocyte that stimulates the production of antibodies by B cells when an antigen is present, and stimulates division of B cells and cytotoxic T cells

Immune Principles

1. Memory2. Specificity

Memory Immune Principle

Once primed by immunogen, rapid response to immunogen

Specificity Immune Principles

Reacts specifically with challenging immunogen

Classes of Immunoglobulins

1. IgM2. IgG3. IgA4. IgE

IgM (M as in Morning, Morning is early)

Early response, effective in defense against baceria infections

IgG (Greatest or major immunoglobulin)

Major immunoglobulin, lasts for years; cross placenta

IgA (Secrete out your Ass)

Found in body secretions

IgE (When I have allergies, I sneeze and say Excuse me)

Involved in allergic responses

Immune Disorders

1. Agammaglobulinemias2. Severe-Comined Immunodeficiency (SCID)3. Athymic Nude mice4. HIV--AIDS

Blood Type = Antigens (Type A blood has A antigens, Type O has none)Antibodies = opposite of blood type (Type A has anti-B Antibodies, Type AB has none, Type o has anti-A and anti-B)

ABO blood types, transfusions and incompatibility

Allergic Responses

IgE antibody ataches to blast cells in tissues, binds allergen, and cause blast cells to release pharmacological chemicals

Organ Transplants: HLA complex

Immune system recognize incompatible transplants as non-self and destroy the transplants. Must use immunosuppressive drugs to permit transplants to survive

Autoimmunity: defects in he immune response system

Immune system attacks and destroys selfEx.LupusMultiple SclerosisType 1 DiabetesRheumatoid Arthrits