My Little Fish

Last post I was talking about how Colin was doggie paddling across the pool, well, I can now report that he dives down in the 4 and 5 foot sections to the bottom to retrieve his "torpedo" toy that we bring for water play. His favorite passtime at the pool is jumping in then swimming down to the bottom. Adrenaline junkie comes to mind. Here's a picture of him swimming under water.


BTW...does anyone dare to take my Biology final tomorrow...here is my study guide (10pages long)...wish me luck!

Biology 10 Study Guide Midterm #4

Molecular Genetics

DNA – The DNA double helix is made out of three things, Sugar (Deoxyribose), Phosphate Group, Base (Thymine, Cytosine, Adenine, Guanine…”T, C, A, G”) The bases contain nitrogen.

DNA stretched out from one cell would be about 7 feet long. DNA molecules normally spread throughout the nucleus, then become visible when they separate before the the cell splits.

DNA TACCCTCAA
MRNA AUGGGAGUU
TRNA UACCCUCAA
Protein Methionine/Glycine/Valine

DNA Model: Red = Oxygen, Yellow = Phosphate Group, Blue = Nitrogen, White = Hydrogen, Brown = CH3

James Watson and Francis Crick – Discovered DNA molecule in 1953 (Nobel prize winners)

Irwin Chargaff (Chargaff’s Rule) found out that the amount of “A” and “T” and amount of “C” and “G” are equal to each other. If “A” is 50%, then “T” is 50%.

Rosalind Franklin was very instrumental in discovering DNA with her experiments with crystallography (xray photographs), but she died before her 40th birthday and was never recognized by the Nobel prize committee for her contributions. Worked on X-ray Chrystallography. She discovered that if you run a x-ray through a crystal and let photographic paper expose for several weeks you can see the shape of DNA. Watson and Crick stole her research and found out that DNA was shaped like a double helix. (Pg. 113, Fig. 8.1). Double Helix is a twisted ladder shape with rungs in between made up of the bases, T,C,A,G.

DNA Replication: The parent DNA “unzips” itself allowing the mRNA to create a new helix copy. A new strand of DNA is created as free nucleotides fill in holes created when parent DNA double helix unzips. This creates two new double helix’s (an exact copy of the parent DNA). P. 116.

DNA codes for proteins (sequence of Amino Acids). DNA made in the nucleus. Proteins made in the cytoplasm. The info needs to get from the nucleus to the cytoplasm. This is done by the RNA (Ribonucleic Acid).

RNA is single stranded and contains no “T” nucleotide. Instead it has a “U” nucleotide (Uracil) that bonds with the “A” nucleotide in DNA. Sugar in RNA is ribose instead of deoxyribose like in DNA. RNA is the messenger from the DNA in the nucleus to the cytoplasm. Information contained in DNA is first transcribed (transcription) to the MRNA. DNA is transcribed into RNA in the nucleus. MRNA carries the code for a protein from the nucleus to the cytoplasm. This process is called translation. When DNA is transcribed to the mRNA, the mRNA is translated into amino acids in protein. MRNA is “decodeded” to make the protein. RNA has 4 letters to represent nucleotides (A, C, G, U). There are 20 amino acids that are made into codes from base pairing of those 4 letters. Each genetic code is 3 letters long. MRNA codes by using 3 letter base codes. Each letter code will signal to the RNA that a certain amino acide needs to be inserted. Codes are called Codons.

Nucleotides: A unit made of sugar, phosphate and base. All free float in the nucleus.

Complimentary Base Pairing is when a molecule unzips and makes an exact copy of itself by using mRNA to translate the protein to the cytoplasm. Amino acids do not recognize the three letter codes on the MRNA. If the code on the mRNA is UCG (Serine), the mRNA must use “transfer” RNA (tRNA) which is shaped like a clover, to communicate the message to the cytoplasm.

MRNA gets captured by Ribosomes which is then translated into protein when tRNA lands on ribosomes (P. 131). A peptide bond is then formed by bonding two amino acids together on the ribosome. When the protein is complete a stop code is inserted by the mRNA to the tRNA and the duplication of the DNA is stopped.

Diploid Number = 46 Chromosomes
Haploid Number = 23 Chromosomes from each parent (egg or sperm)

Mitosis (division of the cell’s nucleus) is the most crucial part of cell division. Process of cell division: Prophase, Metaphase, Anaphase, Telophase, Cytokinesis (splitting of the cytoplasm). P. 143, 148, 149.

Interphase: Growth, DNA & chromosome synthesis

Chromosomes - Everyone has 46 chromosomes (23 pairs) in each of our cells. Chromosome = One DNA molecule, plus proteins. Egg has 23 chromosomes, sperm has 23 chromosomes. Combined in a fertilized egg equals 46 chromosomes. Each parent contributes part of the pair. Male = XY and Female = XX

Karyotype – When chromosomes are all laid out in a display (eg. they do this for an amniosentesis study to make sure chromosomes are normal).

Process: Egg and sperm (each with 23 single chromosomes) meet to fertilize an egg creating 46 double chromosomes which then split into a pair of 46 single chromosome chromatids. A Chromatid is one half of a replicated chromosome. The process of getting from 46 chromosomes down to 23 chromosomes is called Meiosis. Meiosis I: A cell in ovary or testes has 46 single chromosomes which doubles to 46 double chromosomes. In each double chromosome there are two copies of that chromosome's DNA molecule.Then one double goes to each new cell (random separation) creating a set of two cells, each with 23 double chromosomes. Meiosis II: Then those double chromosomed cells each create a pair of 23 single celled molecules which will mature into either a sperm or an egg. Meiosis I takes place inside 3 month old fetus, Meiosis II takes place after fertilization. Polar bodies created by Meiosis – Polar bodies disentegrate.

Non-Disjunction: Abnormal chromosome at #21 (Trisomy 21) results in a baby with Downs Syndrome. Occurs during Meiosis (can occur in Meiosis I or in Meiosis II after a normal Meiosis I). Down’s babies have 47 chromosomes. Incidence rises in mother’s after 40 years of age.

Egg and sperm cells are called gametes.

A gene is a basic unit of heredity. We have approximately 25K genes.

Phenotype – The expressed trait (eg. taster or non-taster) or eye color

Allele – Genes have alternative forms, represented as a T or t

Genetics Example:
Parental Phenotype Taster Non-Taster
Parental Genotype (Alleles) Tt tt
Gametes (Do problem on paper)
Offspring Genotypic Ratio 2 Tt and 2 tt
Offspring Phenotypic Ratio 2 Tasters and 2 Non-tasters (2:2 ratio)

If you have a dominant gene and a recessive gene you are heterozygous. Homozygous = same alleles. P. 175 (gene disorders). Complete Dominance is characterized by a 3:1 ratio.

On gene, two alleles, three phenotypes (eg. Rr x Rr (both red flowers with RR = Red, Rr = Pink, rr = white. Mating Pinks will get you 1 red, 2 pink and 1 white (three phenotypes).

Incomplete Dominance P. 171 Fig. 11.10

Melanin - Albino’s do not create melanin in their skin. Approx. 1/20000 are albino. Two normal people can have an albino child. Albino alleles do not code for enzyme (protein) that codes for Melanin. Tyrosine converts to Melanin with help from enzyme.

Phenylketonuria – Phenylalanine converts to Tyrosine. There is an enzyme necessary for conversion. Phenylketnurics do not make this enzyme. Toxin builds up in the body and destroys the nervous system. If you’re born with it, you’re put on low protein diet. Babies are tested at birth.

Sickle Cell Anemia – Approximately 20 different Alleles for the the Hemoglobin Gene. RBC’s look like a sickle. Caused by a one base error in the DNA. The 7th codon DNA is normally CTC, which converts to GAG (Glutamic Acid) by mRNA. In defective gene the mRNA converts it to Valine.

Mutations

Genetic Mutations: Arise through random errors in the DNA. About 1/10th of people carry a mutation that occurred in the sperm or egg. Some mutations are completely hidden and have no effect. Some mutations cause spontaneous abortion or birth defects. Mutations can be in gametes or Somatic (in body cells). Spontaneous mutations take place every day. About 10K bases get knocked out the DNA by thermal motion and are repaired instantly. Chemicals can cause mutations. X-rays and other radiation (are shorter on the electromagnetic spectrum) are harmful.

UV Rays (cannot see them) – Sunlight = 2% UV, 45% visable, 53% infrared. DNA absorbs UV light. When a molecule absorbs radiation (UV) it causes damage to the DNA. UV light is absorbed by the Ozone in our atmosphere. Ozone blocks out most UV light. Ozone is being depleted. UV absorbed by melanin in our skin. Sunscreen absorbs UV rays. New skin cancer rates: 233/100K for whites, 4/100K for blacks (more melanin). UV rays help to make Vitamin D in our skin. Some sunlight is good to prevent rickets.

DNA repair is done by enzymes that “proofread” the DNA and insert missing bases. People with Xeroderma Pigmentosum lack the DNA repair mechanism resulting in severe DNA damage and skin cancers. Genes involved in DNA repair are more likely to become cancerous. If the wrong base is inserted, disease can result.

Electromagnetic Spectrum - The electromagnetic (EM) spectrum is the range of all possible electromagnetic radiation.[1] The "electromagnetic spectrum" (usually just spectrum) of an object is the characteristic distribution of electromagnetic radiation from that object. Radio waves, Microwaves, Infrared, Visable, UV, X-rays, Gamma rays. EM radiation with a wavelength between approximately 400 nm and 700 nm is detected by the human eye and perceived as visible light. A rainbow shows the optical (visible) part of the electromagnetic spectrum;

Enzymes are catalysts that speed up a process.

When cytoplasm divides, it’s called cytokinesis.

Scientific Ethics

The ideal scientist is a good mentor, teacher who imparts ethos of life in science, recognizes student is not just another lab worker, hangs on to primary data and makes it accessible to colleagues, publishes just the right amount, listed as author only if he is the only writer or made sizable contribution to the project, doesn’t take credit for someone else’s idea or work, doesn’t tell about papers not yet published, protects patients (if scientist is a doctor).

**These are all good guidelines to follow in every day life.

Natural Selection

Theory of Evolution says that all organisms have evolved from a common ancestor in a gradual process of change and diversification. Our planet is 4.7 billion years old. Life appeared 3.9 billion years ago. Evolution is a change within a population.

Fossils – Eggs in nests, skin impressions, bones, feces, footprints

Natural selection perpetuates the most adaptive traits. Selectionist thinking – Natural selection drives evolution. New mutations are important as sources of variation on which natural selection can act because if there was no variation, then evolution would not continue.

Natural Selection: Eg. Drug resistant bacteria. Staph Aureus is drug resistant to antibiotics. The antibiotics don’t kill all the bacteria. The strongest survive because they create an enzyme that destroys the antibiotics. These bacteria live on because they are genetically different. Eg.. Insecticide resistance.. Mosquitos resistant to insecticide because they’re making an enzyme that destroys the insecticide.

Three steps in natural selection: 1. Individuals are genetically different. A few are stronger than the rest and give rise to the next generation. 2. Individuals better adapted to current conditions have more offspring. 3. Populations become to be composed of mostly the best adapted individuals.

Natural selection works in two ways: 1. Encourages the deviants (mutants) to multiply and selects against the normals in favor of the mutants. 2. Deviants are weeded out and selects in favor of the normals – rejects the deviants. Eg. Cats introduced into a barn environment where both dark and white mice live. The lighter (mutant) mice were eaten because they are easier to see. The darker mice survive because they can hide better. This is true if the environment stays the same (stable). It doesn’t pay to be different in this situation.

Artificial Selection - It should be emphasized that there is no real difference in the genetic processes underlying artificial and natural selection, and that the concept of artificial selection was first introduced as an illustration of the wider process of natural selection. The selection process is termed "artificial" when human preferences or influences have a significant effect on the evolution of a particular population or species. Indeed, many evolutionary biologists view domestication as a type of natural selection and adaptive change that occurs as organisms are brought under the control of human beings.

Evolution (from lab)

Earth formed 4.5B, Prokaryotic cells 3.5B, Eukaryotic cells 1.5B, First animals 750M, Dinosaurs extinct 65M, First humans appeared 100-200K years ago

Fossil Formation - Mollusk specimens embedded in rock were covered by sand and were cemented together by minerals in the water. Wood and bone specimens were covered by sediment before they could decay; water then leached out and minerals remained and hardened for form the fossils.

Forelimbs of vertebrates contain: Humerus, Radius, Ulna, Carpals, Metacarpals and Phalanges in some capacity. They are similar because they share a common ancestry and have evolved over time to a variety of functions.

Vestigal Structures – (Remnant body parts, stumpy legs, etc.) Left over from previous ancestors

Comparative Anatomy – Homologous: Structures that have same evolutionary origin. Analagous – All things with wings. Wings perform same function, but no common ancestor.

Ancestors of birds and mammals were the dinosaurs and reptiles.

Evolution (from textbook)

Evolution gave rise to all of life’s key features and characteristics and is the guiding principle that unifies the study of biology. Evolution demonstrates unity because evolutionary change has taken place along the branches of a single “family tree”. Evolutionary change has also led to the variety of lifeforms we have on Earth. The most important process by which evolution occurs is natural selection.

The discovery of feathered dinosaurs supports the theory that birds evolved from dinosaurs

Darwin was led to his ideas about evolution from his experiences on this voyage on the Beagle which included discovering snakes with rudimentary limbs, a snake that rattled its tail like a rattle snake, but it had no rattles and made no noise, penquins used their wings to paddle instead of to fly and several types of finches that when separated developed differently. He also saw that it was not arbitrary when individuals died without reproducing. It was evolution by natural selection “survival of the fittest”.

Malthus influenced Darwin with his statement, “it may be safely pronounced, therefore that human populations when unchecked goes on doubling eveyr 25 years or increases in a geometrical ratio.”. However populations do not multiply unchecked because individuals die in every generation and most do not reproduce.

In 1858 Darwin and Wallace each described the same mechanism for evolution in remarkably similar papers (natural selection)

Evolution takes place on a population level and is not change within specific individuals, but does act on individuals. Evolution is a change in the genetic makeup of populations over generations.

When penicillin attacks bacteria in blood, some mutant bacteria survive to pass along their mutant alleles to the next generation. The population of the bacterium has changed due to natural selection. The new generation can metabolize the antibiotics and are therefore resistant to the effects. Penicillin did not cause the mutation, but it favored the resistant strains so they could live on.

Biologists uniformly agree that evolution occurred in the past and is still occurring today.

Embryos and Development

Fertilized egg develops into an Embryo through this process: Fertilized egg, cleavage, morula, blastula (hallow ball of cells), early gastrula, gastrula, embryo. This process is easily seen in animals where fertilization takes place outside the body. (P. 500-501). This process takes approximately 7 days for a human fertilized egg to become an implanted embryo. Blastocyst becomes an embryo in the human.

Up through blastula stage the cells are NOT determined, meaning all the cells are not yet designated to become an arm, leg or brain tissue. Cells in gastrula ARE determined to form specific body parts.

Stem cells are in everything up through the blastula stage. Stem cells can be embryonic (pluri-potent). Researchers can now make pluri-potent cells from regular skin cells. Adult stem cells are not embryonic and are not as potent. Stem cells help you heal. Stem cells can be stationary in certain tissues (skin & bone marrow) or migratory in the blood (can go to a wound site to help the body heal).

Regenerative Medicine: The growing of new tissues to replace damaged parts. Eg. growing skin for skin grafts which eliminates the need for a doner. Sometimes this process is called therapeutic cloning (uses stem cells).

Dolly the sheep (P.145) proved that cells beyond the Gastrula phase are not always predetermined. With Dolly the nucleus was taken from the mother egg. An adult doner nucleus was implanted in that egg, the cells were fused by some sort of electrical charge (no fertilization took place from a father) and then the fertilized egg was implanted into a donor mother. The result was a complete clone of the adult donor of the nucleus. This process was tried with 277 eggs and only one success (Dolly…named for Dolly Parton).

CC was a carbon copy cat. Even though genetic material was the same the coloring was different because there are still traits that are not entirely coded in the genes and there is a small amount of DNA in the cytoplasm that is transferred to the offspring.

Fingerprints of identical twins are not the same. Identical twins are from one egg (monozygotic) that splits into two and have the same exact genes. Fraternal twins form when two eggs (dizygotic) are fertilized. The offspring are no more alike than a normal brother and sister.

Biotechnology

Biotechnology: The use of organisms to provide goods and services. Traditional methods include selective breeding. Selected for traits that are desirable. Eg. Kale, cabbage, broccoli, kolabi, cauliflower are all the same species that were selectively bred for their different characteristics. Individuals are genetically different. Corn has been selectively bred from a weed on the side of the road into the corn we know and eat today. Corn such as we eat was not found naturally in nature, it was selectively bred. Natural Selection: Adaptive traits are perpetuated by nature.
Genetic Engineering: Includes cloning (reproductive technologies).

Recombinant DNA- DNA from one species combined with another species. Genetic engineering uses recombinant DNA.

Transgenic organisms (GMO’s) are genetically modified. Some are harmful, some are beneficial.

GMO Examples

Human Insulin: Diabetics use GMO insulin “pure human insulin” grown in bacteria because bacteria grows faster than human cells; more efficient at reproduction

Human Clotting Factor: Transferred and grown in sheeps milk. Collagen transferred to sheep who create milk with the protein in it for Clotting Factor which is processed out and then used for humans.

Edible Vaccines: Bacteria transferred into potatoes; people eat the potatoes and are then immune to such things as E.Coli (which kills thousands every year)

Bt put into the corn plants which makes the corn resistant to catapillars that eat the plants. Catapillars stomachs blow up after eating the modified plants. Pollen from these plants is spreading out of the crop zone and is killing non-predatory catapillars such as Monarch catapillars.

Herbicide resistance: Bacteria put into plants so that the plant produces an enzyme that kills the herbicide.

Transfers of genes between plants

Golden Rice: Has gene for beta-carotene which is a pre-cursor for Vitamin A. Millions of people around the world are deficient in Vitamin A, this solves the problem. It’s NOT on the market yet.

Vitamin E is being added to oils

Transfer of genes between animals

Genes for spider silk has been transferred into goats. Goats produce milk that contain the spider silk genes. Spider silk is processed out of the milk.

Restriction Enzyme: Will cut DNA at a specific DNA sequence. These enzymes come from bacteria. A virus that attacks bacteria is called a phage. Bacteria need these enzymes to control viruses that try to kill them.

Plasmid – Circular piece of DNA located in the cytoplasm of bacteria. Carries genes that assist bacterial survival in certain environments, such as gene for antibiotic resistance. Mix plasmid with genes, bacteria will take up foreign genes and begin to use them in their own bodies.

Gene Therapy: Correcting genetic defects caused by certain diseases

Somatic Gene Therapy - the gene is introduced only in somatic cells, especially of those tissues in which expression of the concerned gene is critical for health. Expression of the introduced gene relieves/ eliminates symptoms of the disorder, but this effect is not heritable as it does not involve the germ line. At present, somatic cell therapy is the only feasible option, and clinical trials addressing a variety of conditions have already begun.

SCID – Severe Combined Immune Deficiency: “Bubble Babies”, immune system does not work because they lack a certain enzyme because the gene that codes for that enzyme is defective. Without the enzyme, a toxin builds up and destroys their WBC’s. Gene therapy has corrected the problem. They take WBC’s from the bone marrow and put the gene for the enzyme into a virus that circulates though their body. WBC’s are no longer destroyed and the person can live a normal life.

Germline Engineering: In the case of germ line gene therapy, germ cells, i.e., sperm or eggs, are modified by the introduction of functional genes, which are ordinarily integrated into their genomes. Therefore, the change due to therapy would be heritable and would be passed on to later generations. This new approach, theoretically, should be highly effective in counteracting genetic disorders. However, this option is prohibited for application in human beings, at least for the present, for a variety of technical and ethical reasons.Corrects defects in the sperm and egg so that the defect cannot be passed along or makes sure that certain genes are passed along. Eg. elevated milk production in cows, Sheep that synthesize human clotting factor.

“Designer babies” – Choosing certain attributes before birth.

Each cell has all 46 chromosomes and 25K genes in both the blastula and gastrula. In early gastrula stage certain genes get turned off ad others get turned on (activated). Eg. a pancreas cell gets triggered to become a pancreas and all other genes are turned off so that it won’t also try to become brain tissue, etc. Blastula cells are pluri-potent (with many potentials).

Genome - In biology the genome of an organism is its whole hereditary information and is encoded in the DNA (or, for some viruses, RNA). This includes both the genes and the non-coding sequences of the DNA. More precisely, the genome of an organism is a complete genetic sequence on one set of chromosomes; for example, one of the two sets that a diploid individual carries in every somatic cell.

The haploid human genome (23 chromosomes) is estimated to be about 3 billion base pairs long and to contain 20,000-25,000 distinct genes.

Plant Structure and Function
Plants defend themselves with toxins. Modern day plants have wild ancestors that are poisonous. Eg. Wild lettuce is very bitter and toxic. (P.314- Fig. 17.1). About half of a plant is visable. The other half lives below the ground.

Roots absorb water & nutrients and anchor the plant in the ground. Tips of roots have root hairs that maximize the surface area of the roots to absorb water, etc. The stem supports the leaves. The leaves photosynthesize (make sugar from the sunlight).

Xylem and Phloem are grouped together in a vascular bundle. These spread to the leaves in the form of veins (P. 325, Fig. 17.15).Vascular plants have vessels for the water to travel in throughout the plant. Tissue in the stem called the Xylem which are hallow tubes (P.318, Fig. 17.5) which carry water and nutrients upward. Plants use sunlight to make sugar which travels downward to the roots and leaves. Phloem tissue carries the sugar downward to roots.

How does water get up to the top of tall trees? World’s tallest tree is in Montgomery Woods is 360 + feet tall. (Pg.328, Fig. 17.3). Water evaporates from the leaves and as this evaporation takes place, more water is pulled upward from the roots and vessels causing more water to be pulled into the root system from the soil around the roots. Called transpirational pull.

Growth occurs at the tips of the top of a tree. Trees do not add cells at the bottom. Clusters of dividing cells called meristems. Apical meristems are at the tip of the meristems.

A layer of cells between the bark an the wood called cambium (meristem). Cells dividing on the inside of the wood and cells dividing on the outside of the bark. (P. 381, Fig. 17.11)

To make a plant more bushy, instead of taller, snip the terminal bud. Plants send up a hormone when the terminal bud is cut to tell the lateral buds to start growing.

Grass cells multimply at the bottom of the plant to contend with grazing animals and lawn mowers. Meristems in grasses are at the bottom of the plant.

If a tree is cut down, but the stump is left intact, little suckers will come up.

The top and bottom of the leaf is covered by the epidermis layer of cells. Then a layer of waxy material on top of the leaf to protect the leaf from evaporation of water off the leaf.

Mesophyll – Shaped like little cucumbers are tightly packed in the plant cell. Palisade – tightly packed. Spongey layer – loosely packed, lots of water vapor in this area.

On the bottom of the leaf cell there are little holes called stomates (stomatas) surrounded by guard cells. Stomates close at night or when it’s really hot so they don’t lose water. Stomate opens by inflating guard cells with water. Closes the hole by removing water from the guard cells (process called transpiration).

About 99% of water a plants takes in is from it’s roots and goes out through the leaves. It’s wasted by the plant.

Chloroplasts are inside the cells of all layers in the plant.

Why are plants green? (P.84, Fig. 6.2b). The electromagnetic spectrum wave lengths are measured in nanometers. 1nm. = .001 um. The spectrum includes violet, blue, green, yellow, orange, and red. Chlorophyll is the green pigment that absorbs light. Chlorophyll removes (absorbs) all colors except the green and yellow are not absorbed so that’s what we see.

Flowers
Stigma: Sticky tip of the pistil (receptor of pollen)
Carpel: Female reproductive organ
Style: Pathway for pollen tubes from stigma to ovules
Ovary: Female ovules
Stamens: A filament topped by an anther, where pollen is produced
Pollen: Contains male gametes
Sepal: Outer leaves near the base of flower
Petals: Colored part of flower (pretty part)
Pistils: Made up of female sexual organs (carpels)

Mutualistic: Two species have a relationship and both survive and both benefit from the relationship. Eg. Flower and bees. Bees get food, flower gets pollinated.

Not-Mutualistic: Not all seed dispersal is mutualistic. Eg. Burrs on a dog, doesn’t benefit the dog at all.

Earlier Information

Scientific Method: Observation, Hypothesis, Experiment, Conclusion. Scientific method is useful in everyday life. A scientific theory is a hypothesis that has been tested and proven.

Biology helps you understand your body, become an informed citizen, enrich your appreciation of the world.

Living things: Are complex and organized, grow and reproduce, respond to stimuli, aquire materials and use energy and use DNA to store information.