BIOL 100 Section 2

Hox Gene Cluster

Linear arrangement of Hox genes on a chromosome; the order of genes on the mirrors their progressive anterior to posterior expression patterns

Developmental Biology

-Environmental teratogens cause developmental abnormalities -Ethical concerns regulate cloning and stem cell research -Comparative embryology unravels questions about evolution -Stem cell research hopes to discover cures for diseases An embryo's environment is mainly influenced by its connection to the mother's blood stream through the umbilical cord and placenta. If beneficial things like nutrients and oxygen can pass from the mother to the embryo, so can harmful things like teratogens.

Synthesis (S)

The S phase is when DNA synthesis takes place. At the end of S phase, each chromosome has two sister chromatids

DNA Information Storage

The ability of DNA to act as a store of information comes from its nucleotide structure. As we have learned, there are four distinct nucleotides that can be used to make a molecule of DNA, Adenine (A), Thymine (T), Guanine (G) and Cytosine (C). The order of nucleotides in a strand of DNA is not random; the A,G,C and T nucleotides act as a molecular alphabet. A particular sequence of these nucleotides within a strand of DNA creates a "gene", thus you may have also heard of DNA containing a "genetic code" or "genetic information". These genes contain the information necessary to make a protein.

Multipoint Stem Cells

can form limited cell types. They are partially differentiated, giving rise to cells that have related functions or will form parts of the same organ system. For example, hematopoietic stem cells form all types of blood cells (red blood cells, T-cells, B-cells, neutrophils, macrophages, etc.) but, they cannot form brain cells or muscle cells. Human multipotent cells are more commonly known as adult stem cells. They are found in several organs and self-renew to replenish old and damaged cells.

Unipotent Stem Cells

can only differentiate into a single cell type - their own. Unipotent cells are still considered stem cells since they can self-renew. An example of unipotency is skin cells, which divide to replace the millions of dead skin cells we slough off every day.

Frameshifts

A DNA mutation that leads to a shift in the way the nucleotide sequence is read; often the result of insertion and deletion mutations Insertion and deletions can lead to a shift in the way the nucleotide sequence is read. Remember, nucleotides are read in sets of three as codons. Therefore, if nucleotides are inserted or deleted, it can change the way the nucleotides are read. If one of the letters is deleted, the sentence does not make much sense - just like the codon sentence does not always make sense when nucleotides are inserted or deleted.

Anemia

A condition when your blood has lower than normal red blood cells or the red blood cells are low in hemoglobin

Zygosity

A description of the zygosity of our alleles, that is to say, how they are written in our genetic code, is known as a genotype.

Genotype

A description of the zygosity of our alleles, that is to say, how they are written in our genetic code, is known as a genotype. -how the alleles are written in our genetic code.

Silence Genes

An alternative route to cancer is to silence genes that are normally active. This includes tumor suppressor genes such as BRCA1. These genes are normally active to ensure the cell cycle is properly regulated. Silencing of these genes leads to an overactive cell cycle progression.

Elongation

An mRNA molecule is synthesized using base pairing rules to make a complementary strand to the template strand (which is a copy of the coding strand with U instead of T). RNA polymerase moves along the DNA elongating the mRNA molecule based on the nucleotides present in the DNA.

Genetic Counseling

Genetic counseling is applied population genetics, for it relies on both pedigree analysis (standard genetics) and knowledge of the frequency of a particular allele in the population at large to calculate the likelihood of inheriting a genetic defect. Thus evolution has real applications in our lives.

Nervous System

The nervous system is the first organ system that begins to form, but one of the final ones to complete. The nervous system is derived from ectodermal cells (the "outside" germ layer) and forms on the dorsal (back) side of the embryo. The first step of nervous system formation is called neurulation

Prometaphase

The nuclear envelope degrades. Thread like structures called microtubules extend towards the middle of the cell, where some bind to the DNA via a central structure called a kinectochore.

Epigenetic Modifications

Chemical modifications to the DNA or the histones alter the structure of the chromatin without changing the nucleotide sequence of the DNA. Such modifications are described as epigenetic. Changes to the structure of the chromatin have a profound influence on gene expression. If the chromatin is condensed, the factors involved in gene expression cannot get to the DNA, and the genes will be switched off. Conversely, if the chromatin is 'open', the genes can be switched on if required.

Carcinogen-induced Mutations

Chemicals, known as carcinogens, can induce mutations (changes in DNA), some of which may cause cancer. Known carcinogens include chemicals present in tobacco smoke, alcohol, ultraviolet light from the sun (and tanning booths!), and radiation from sources such as X-rays. Different carcinogens may promote different cancers, generally influenced by the route of exposure. For instance, tobacco smoke is more likely to cause lung cancer than ultraviolet light, which can promote skin cancer. Our knowledge of carcinogens is constantly expanding and it should be noted that this list now includes many chemicals that were once thought to be safe. Just as in the past, chemicals that we are now exposed to daily may one day be known carcinogens. -chemicals that can induce mutations such as smoke, alcohol, ultraviolet light from the sun, etc.

Fetal Alcohol Syndrom (FAS)

Children with FAS have characteristic facial defects like wide set eyes, a flat face, and a small head. But the most serious problem is the potential for mental retardation. Alcohol can cause neurons to die during fetal brain development, explaining why children with FAS have below-average IQs and reading and math abilities. These mental problems carry over into adulthood, since many adults born with FAS have problems handling money, learning from experiences, and coping with the demands of normal life.

Blastocyst

Cleavage ends with the formation of a hollow ball of cells called the blastocyst. The center cavity is called the blastocoel. The blastocyst contains two types of cells. (1) The outer trophoblast cells help form the placenta and other extra-embryonic tissues, but do not contribute to the embryo itself. (2) Cells of the inner cell mass are the precursors of all future cells of the embryo's body and are more commonly known as embryonic stem cells. The separation of function between the trophoblast and inner cell mass is the first evidence of differentiation, or specialization, in the embryo. Hollow ball of cells formed during cleavage; first evidence of differentiated embryonic cells.

Somatic Cell Nuclear Transfer (SCNT)

Cloning technique involving transfer of a nucleus from an adult somatic cell into an enucleated egg

Inner Cell Mass (ICM)

Collection of blastocyst cells known more commonly as embryonic stem cells; will divide to form all future cells in the embryo's body

Acrosome

Compartment in sperm head containing enzymes that penetrate the zona pellucida during fertilization A sac, called the acrosome, containing enzymes that allow the sperm to enter the egg. If sperm binding is successful, the acrosome releases enzymes that chew a hole through the zona pellucida.

Treatment for these Diseases

Currently, there is no cure for either of these terrible diseases, and treatment focuses primarily on managing painful symptoms to keep patients as comfortable as possible. For sickle cell anemia, blood transfusions are a common treatment to replenish the body's red blood cells and may help decrease strokes. Constant doses of oral antibiotics to prevent acute chest syndrome is prescribed for infants and children until age 5. More recently, the anti-cancer drug, hydroxyurea, has been used to manage sickle cell crises. As for CF patients, the main goals are to keep bacterial infections in the lung to a minimum and keep the mucous levels low. To help clear mucous from the lungs, patients go through a bronchial draining therapy which involves the patient being put into a position for optimal clearing and someone clapping on their back to loosen and dislodge mucous from the lung. Medications are also used to open airways and decrease mucous. A specific diet is used to counteract the digestive complications.

CFTR

Cystic Fibrosis Transmembrane conductance Regulator protein; it is the gene that is mutated to cause cystic fibrosis.

Nucleotides

DNA and RNA are made up of monomers, which in the case of nucleic acids, are called nucleotides. a single monomer. monomer of DNA and RNA that consists of a 5 carbon sugar, a phosphate group, and a nitrogenous base

Nucleic Acids

DNA and RNA belong to a class of macromolecules known as nucleic acids.

DNA Makeup

DNA and RNA belong to a class of macromolecules known as nucleic acids.DNA and RNA are made up of monomers, which in the case of nucleic acids, are called nucleotides. There are three parts that make up a nucleotide: a 5 carbon sugar, a phosphate group, and a nitrogenous base.

5 Carbon Sugar (Pentose)

DNA and RNA have a 5 carbon sugar (also known as pentose) as the center of their nucleotides. The 5 carbons of the sugar ring are labeled 1', 2', 3', 4' and 5' based on their position in the ring with respect to the central oxygen (O). Using this numbering system we can indicate the location on the carbon ring where other molecules are attached.

Metaphase II

Chromosomes are positioned in the middle of the cell, as in mitosis. Microtubules bind the kinetochores of the sister chromatids.

Metaphase I

Chromosomes line up at the middle of the cell and are bound by microtubules

Endoderm

(inside): lining of digestive and respiratory systems

Allele

Each copy of a gene represents an allele, which is an alternate form of a gene. represented by each copy of a gene and is an alternate form of a gene.

Trophoblast

Outer layer of cells of the blastocyst; some of these cells will help form the embryonic component of the placenta

Ribosome

Site of protein synthesis where proteins are translated from mRNA

Termination

When RNA polymerase reaches the terminator, RNA polymerase dissociates from DNA, and an mRNA molecule has been created. Transcription is complete.

Zygote

diploid (2N) zygote Specific name for a single-celled embryo that is fertilized but has not yet divided

2 Types of Cell Division

mitosis & meiosis

Thomas Malthus

"An Essay on the Principle of Population" saying that if everyone had a lot of children and every one survived to adulthood we would have a huge population, and this does not happen because there is regulation. He argued that population growth generally expanded in times and in regions of plenty until the size of the population, relative to the primary resources, caused distress and populations collapsed due to war, disease, famine etc.

Charles Lyell

"Principals of Geology". The central argument in "Principles" was that the present is the key to the past. Lyell wrote that geological remains from the distant past can, and should, be explained by reference to geological processes now in operation and thus directly observable. His interpretation of geologic change as the steady accumulation of minute changes over enormously long spans of time was a powerful influence on the young Charles Darwin.

Cystic Fibrosis (CF)

(Genetic Disease) A genetic disease affecting the mucous glands of the lungs and digestive system. CF is a progressive disease that affects the mucous glands of the lungs, small intestine, and pancreas as well as the sweat glands. CF patients often lose excessive amounts of salt when they sweat leading to an imbalance of minerals in the blood and abnormal heart rhythms. Mucous in the lungs of CF patients is also very thick and sticky. Having a thin layer of mucous lining the lungs and intestines is important for lung and digestive function, but when the mucous becomes too thick to be removed regularly, it serves as a playground for bacterial infections. CF patients typically have chronic bacterial infection that are difficult to fight and can lead to lung damage. The thick mucous found in the pancreas can block the pancreas from secreting digestive enzymes into the intestine leading to malnutrition. Other complications of CF include sinusitis (inflammation of nasal sinuses), clubbing of fingers and toes (rounding of the fingers and toes), coughing up blood, and liver disease. Lung disease is often the cause of death in CF patients and the average lifespan of a CF patient is 30 years. CF is most common among caucasians with ancestors from Northern Europe. The most common CF mutation is the result of a deletion of three nucleotides resulting in a loss of one amino acid in the coded protein. Seventy per cent of the mutations involved in CF are the result of a three- nucleotide deletion leading to the deletion of one amino acid in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. The normal CFTR protein is a chloride channel protein in the membrane of cells that line the lungs, liver, pancreas, intestine, and reproductive organs. This protein is essential in maintaining the balance between sodium and chloride ions in these cells. The most common mutation associated with CF is the deletion of the three nucleotides that encode for phenylalanine. The deletion of phenylalanine causes the protein to misfold and it is marked for degradation. Thus the protein never makes it to its proper place within the cell and it has lost its function. The production of thick mucous in the lungs and digestive system leads to the complications of CF. How does a mutation in a chloride channel protein create thick, sticky mucous? -The deletion of three nucleotides in the CFTR sequence leads to the deletion of one of the amino acids in the CFTR protein (phenylalanine). - The CFTR protein is misfolded and loses function. - The membranes of the cells that line the lungs, pancreas, etc. lacks a functional chloride channel protein (See Figure 13). - These cells lose the ability to maintain the balance between sodium and chloride ions within the cell. This balance maintains the usual healthy thin layer of mucous in the lungs and digestive track. - The sodium/chloride imbalance leads to the build up of thick mucous. As we have discussed, this thick mucous is at the core of the symptoms and complications of CF that is marked by chronic lung infections and lung damage

Sickle Cell Anemia

(Genetic Disease) Sickle-cell anemia is a serious blood disease in which red blood cells (RBC) take on a sickle or "C" shape instead of the normal round shape.In this disease, the abnormal shape of the RBCs causes the RBCs to clump in blood vessels blocking blood flow to various organs and tissues. The blockage of blood vessels can cause severe pain in the blocked area, a condition referred to as a "sickle cell crisis." A "crisis" is marked by sudden pain throughout the body particularly affecting bones, lungs, abdomen, and joints. There are several complications associated with this disease including anemia (a condition when your blood has lower than normal red blood cells or your RBCs have low levels of hemoglobin marked by fatigue, shortness of breath, and weakness), hand-foot disease (swelling of the hands and feet due to blocked blood vessels), infections, acute chest syndrome (pneumonia-like infection caused by sickle cells getting trapped in the lung), and stroke. Sickle cell anemia primarily affects people from or with decedents from sub-Saharan Africa or other areas where malaria is prevalent. Sickle-shaped cells are more resistant to malaria infection and arose as an adaptation to the disease. Sickle cell anemia is the result of a single nucleotide mutation leading to a change in one amino acid in one of the proteins that make up hemoglobin. The most common gene mutation leading to sickle cell anemia is a single nucleotide substitution that changes one amino acid in the hemoglobin beta gene (or HBB). There are two protein chains that make up hemoglobin, the protein that carries oxygen throughout the body via red blood cells, alpha chains and beta chains. The HBB gene makes up the beta chains. The most common HBB mutation is called Hb S, which is a point mutation that leads to an amino acid substitution of a valine instead of a glutamic acid. This single substitution causes the hemoglobin protein to bind together abnormally forming long fibers, which cause the red blood cells to "sickle". The main complication of Sickle Cell Anemia is that the sickle-shaped cells can clump up and block blood vessels leading to several symptoms that we have discussed, but how does that ONE mutation in the HBB gene actually cause the disease? - As we saw in the previous slide, the single nucleotide substitution changes one of the amino acids in the protein sequence - This amino acid substitution causes hemoglobin proteins to bind together to form long fibers inside the RBC. - This abnormal binding of hemoglobin proteins inside of RBCs lead to the sickle shape of RBC cells. - The sickle shape of the RBCs are sticky and can block blood vessels. - Blockage of blood vessels lead to most of the symptoms and complications of the disease - Therefore, this single nucleotide mutation has a profound affect on the normal function of the protein, which leads this disease.

Anaphase

(Greek "Ana" = up): During anaphase, the sister chromatids are pulled to opposite ends of the cell by the microtubules (A for action). The cell takes on an elongated shape. By the end of anaphase,each pole of the cell has a complete (and equivalent) set of chromosomes. -the stage of mitosis when chromosomes separate in a eukaryotic cell. Anaphase begins abruptly with the regulated triggering of the metaphase-to-anaphase transition; and at this point the anaphase becomes activated.

Metaphase

(Greek "Meta" = between). The chromosomes have lined up in the middle of the cell (M for middle). Each sister chromatid is attached to microtubules that are anchored at opposite ends of the cell. -a stage of mitosis in the eukaryotic cell cycle in which condensed chromosomes, carrying genetic information, align in the middle of the cell before being separated into each of the two daughter cells. Microtubules (one of the components of the cytoskeleton) that had formed in prophase have already found and attached themselves to kinetochores in metaphase.

Prophase

(Greek "Pro" = before): As its name suggests, this step happens before mitosis. The chromatin fibers of DNA get moretightly coiled, condensing into discrete chromosomes that are visible with a microscope -is a stage of mitosis in which the chromatin condenses into a highly ordered structure called a chromosome (it is at this stage giemsa staining - used for the pathological history diagnosis of malaria and other parasites - can be applied to elicit G-banding in chromosomes) in which the chromatin becomes visible.

Telophase

(Greek "Telo" = end): The cell continues to elongate and nuclei form around the sets of chromosomes found at each pole of the cell. The DNA becomes less tightly coiled. Cytokinesis, the division of the cytoplasm, generally occurs during this time, dividing one cell into two daughter cells. -a stage in either meiosis or mitosis in a eukaryotic cell reversing the effects of prophase and prometaphase events.

The Template Strand

(The Noncoding Strand) because double stranded DNA is anti-parallel this strand has the nucleotide codon sequence opposite of the coding strand. This strand is the one used to make mRNA during transcription. The DNA strand that forms the template for the transcribed mRNA. This strand is the opposite strand of the coding strand. Runs 3'-5'

Double Stranded DNA

(double helix) - two DNA strands running in opposite directions connected by base pairing

Mesoderm

(middle): circulatory system, reproductive system, kidneys and urinary system, bone, muscle, tendon

Ectoderm

(outside): skin, pigment cells, nervous system including brain, and spinal cord

Evolution

-Biological evolution is descent with modification -Fossils are removed preserved remains from organisms of the remote past -Neo-Darwinism combines natural selection and Mendelian inheritance -Charles Darwin wrote "On the Origin of Species" The fact that all life forms on earth share a common ancestor represents the central theme of evolution. It is through change with modification that common ancestry is responsible for the magnificent diversity that now exists on this planet. In other words, evolution tells us that humans and other life forms are all distant cousins. -decent with modification; change over time through genetic inheritance.

Cell Division

-Cell Cycle is a series of events that allows cell replication -Cell cycle checkpoints control the order of events during cell division -Meiosis is the process that creates gametes (sperm and eggs) -Mitosis is the process by which cells divide Fertilization triggers initiation of the zygotic cell cycle, resulting in cell division and a rapid increase in cell number. The single celled zygote divides into a 2-cell embryo, which divides into the 4-cell embryo, and so on. Cell division during the cleavage stage generates special embryonic cells called blastomeres.

DNA

-DNA strands are made of nucleotides --Copies of DNA are made by replication -modification of nucleotides leads to mutation -long double strands of DNA (called chromosomes) are called a genome DNA is the molecule that stores information long-term. It is also the molecule that transmits information to new cells so all cells carry the same information. DNA holds all of the information required to run a cell. It is also the molecule that is passed down from cell to cell so that every cell has the same information. short for Deoxyribonucleic acid, a polymer of nucleotides that stores cellular information As you learned, DNA is made of a string of four different nucleotides (Adenine, Guanine, Thymine, Cytosine) that can be combined in any order. The nucleotides are transcribed from DNA to RNA.

Differentiation to Organs

-Differentiation transforms stem cells into specialized cells -Differentiated cells form tissues -Different tissues form organ systems -Tissue-specific gene expression drives differentiation

Embryonic Development

-Fertilization creates new through fusion of egg and sperm -Implantation establishes a connection between an embryo and mother -Gastrulation organizes the body plan -Cleavage increases cell number through cell division (Mitosis) In order for an embryo to properly develop, it must: 1. Originate from the union of egg and sperm (Fertilization). 2. Grow via cell division to increase total cell number (Cleavage). 3. Organize cells to establish the body plan (Gastrulation). 4. Specialize cells to perform diverse functions (Differentiation). 5. Rearrange cells to build tissues and organs (Organogenesis). Embryonic development begins at the point of fertilization - the fusion of a haploid sperm and haploid egg to create a diploid zygote. Sperm must overcome many barriers to successfully fertilize an egg, including a long-distance swim, capacitation, and species-specific recognition of the egg. The egg prevents polyspermy by modifying proteins on its zona pellucida, preventing the binding of additional sperm.

Genetics/ Epigentics

-Genetics studies how traits are encoded by DNA and how they are inherited -Phenotype describes the manifestation of a trait -Epigenetic modifications alter gene expression without altering the gene itself -Genotype describes the genetic composition of an organism

Evolution and Us

-Hominids are human like species -Bigger brains gave hominids a major adaptive advantage -The concept of evolution is essential to understanding biological mechanisms -Bipedalism changed hominid development

Mutation and Disease

-Mutations in DNA can create changes in protein -Loss or alteration of protein function can lead to disease -Specific gene mutations determine which disease may occur -Abnormal proteins can influence phenotype (function and structure)

Gene Expression

-Nucleotide sequence encodes amino acid sequence -mRNA carries the genetic code for protein synthesis to the cytoplasm -Translation process makes proteins from mRNA, tRNA, and ribosomes in the cytoplasm -Transcription process creates mRNA from DNA inside the nucleus gene expression is taking the genetic code from the DNA, transcribing it into mRNA, and then translating the mRNA into protein. So when a cell gets a signal from the environment or other cells that it needs more of a given protein, it must first make a copy of the gene that encodes that protein through transcription. Once the transcript is made, the mRNA leaves the nucleus and enters the cytoplasm where it is translated into protein. Gene expression simply means that a gene encoded in DNA is transcribed into mRNA that is then translated into a protein. When a cell needs a particular protein product, that gene will be expressed meaning it will go through all of the processes discussed in this module. The process by which information from a gene (DNA) is made into a functional gene product (protein) using mRNA.

Natural Selection

-Selection changes the traits of a population -Mutations are explained by changes in genotype -Fitness depends on the environment -Gene flow and genetic drift partially explain natural selection the survival in nature of those individual and their progeny best equipped to adapt to environmental conditions.

3 Objections to Darwin's Evolution Theory

1. He could not explain how characteristics were inherited. 2. There are situations in which gradual evolution can not explain the changes seen. 3. It is sometimes difficult to explain that evolution can happen by chance. Then there was the question of origin of man. In 1859, Darwin had only said "Light will be thrown on the origin of man". After Darwin published The Descent of Man in 1871, he was depicted in caricature with an ape body, identifying him in popular culture as the leading author of evolutionary theory.

3 Mechanisms of Variation

1. Mutations 2. Genetic Drift 3. Gene Flow

Requirements for Cell Division (Cell Cycle)

1. Signal - Cell division is a highly regulated process. Cells must receive signals, either internal or external, to divide. 2. Replication - After a division, each daughter cell has anequal amount of DNA to each other as well as to the parent cell. For this to occur, the parent cell must first duplicate its DNA. 3. Segregation - The DNA of the parent cell is equally allocated to each of the daughter cells 4. Cytokinesis - The cytoplasm and organelles must be divided between the daughter cells. These events consistently occur in the same order, called the cell cycle.

3 Things That Can Be Explained by Using the Bell Shaped Curve of Trait Distribution

1. Stabilizing selection: average trait value is going to stay the same. 2. Directional selection: one side or the other of your bell curve is selected for. 3. Disruptive selection: the two sides of the bell curve is favored but the middle is not.

Patterns of Macroevolution in the Tree of Life

1. Stasis 2. Character Change 3. Lineage Splitting 4. Extinction

Evidence of Evolution

1. The fossil record 2. Common structures and behavior 3. Biogeography 4. Molecular evidence

Evolutionary Biology's Contributions to Society

A. Human Health and Medicine: Sickle-cell Anemia and Antibiotic Resistance B. Agriculture and Natural Resources: Plant and Animal Breeding and Pest Resistance C. Environment and Conservation: Bioremediation and Biodiversity Crisis.

Adaptations for Upright Bipedal Movement

1. Thigh bone slopes inward from the hip to knee, placing feet under the center of gravity. 2. Gluteal abductor muscles are well-developed on the side of the hips to contract and prevent bodies toppling to one side when all the weight is on one foot in mid-stride. 3. The foot is specialized with an arch that acts as a shock absorber and weight bearing platform. 4. The spine has a characteristic double curve, which brings the head and torso into a vertical line above feet. 5. The surfaces of the joints in legs and between vertebrae are enlarged, which is an advantage for bearing weight. 6. The hole through which the spinal cord enters the skull, called the foramen magnum, is near the center of the cranium, allowing the head to balance easily atop the spine rather than toward the back of the cranium as in chimps.

Stages of Progressive Differentiation

1. Totipotent stem cells 2. Pluripotent stem cells 3. Multipotent stem cells 4. Unipotent stem cells 5. Terminally differentiated cells

Evolutionary Principles and Conservation

1. Using phylogenetic information to determine which regions contain the greatest variety of biologically unique species. 2. Using the data and methods of evolutionary biogeography and the study of organisms' distributions to identify "hot spots" - regions with high numbers of geographically localized species 3. Using population genetic theory to determine the minimal population size needed to prevent inbreeding depression and to design corridors between preserves to allow gene flow, both of which maintain the ability of populations to adapt to diseases and other threats. 4. Using genetic markers to control traffic in endangered species. These methods have been used to spot illegal whaling, and are routinely used to distinguish illegally smuggled from legally captive-bred parrots. In fact, these birds have such a high market value that insurance companies are requiring DNA fingerprints of pet parrots.

Darwin's Natural Selection (4 Components)

1. Variation 2. Inheritance 3. High rate of Population Growth 4. Differential Survival and Reproduction

Artificial Selection

1. Variation between individuals in traits 2. The variation in some traits heritable 3. Breeders select animals with traits that the breeders like 4. Next generation has more of these traits -a process in the breeding of animals and in the cultivation of plants where a breeder will choose favorable trait and breed the species that posses the favorable trait in order to create a different breed.

3 Great Themes in Biological Science

1.Function 2.Unity 3.Diversity

R.A. Fisher, J.B.S. Haldane, and Sewall Wright

1918 demonstrated that the continuous variation in real populations could be derived from Mendelian principles. Fisher (1890-1962) along with J.B.S. Haldane (1892-1964) and Sewall Wright (1889-1988) demonstrated that Mendelian heredity and natural selection are compatible. Support Neo-Darwinism

Galapagos Finches and Differential Survival and Reproduction (Effects of Drought)

1977, a severe drought occurred on Daphne Major. Plants withered and seeds of all kinds were scarce. Small soft seeds were quickly eaten by the finches, leaving mainly large, tough seeds that finches normally ignore. The drought ended when a small amount of rain fell on the island in January 1978. Over the drought period the proportion of seeds that were big in the island became higher and the birds with bigger beaks that could eat them survived and reproduced. Over generations this resulted in selecting birds with a larger body size that also had a bigger tougher beak. Before the drought, the average beak size of the Geospiza fortis species was 10.68 mm long and 9.42 mm deep. After the drought, it was 11.07 mm long and 9.96 mm deep. The wider and bigger the beak, the more force it can generate. So, the birds that could open the seed and feed on the larger seeds during the time of drought survived, reproduced, and carried the larger beak trait to the next generation. In other words, the large beak trait was naturally selected shows that individuals with traits that fit the environment will survive and will become a greater proportion of the next generation.

Walter Gehring

1994 discovered the eyeless gene, which guides formation of fruit fly eyes. As an experiment, Gehring put a mouse's eyeless gene into a fruit fly, resulting in normal fruit fly eyes (Fig. 25). The same holds true for Hox genes for wings, legs, and even heads. This discovery indicates that animals descended from a single common ancestor that passed along to them a set of Hox genes, used to build a wide variety of forms from just a few basic body plans.

Neanderthal Genome

2006, scientists at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany began working on mapping the Neanderthal genome. The initial thought that Neanderthals were a subspecies of Homo sapiens has been dismissed by analysis and comparison of mitochondrial DNA (mtDNA) from both species and calculates that the closest ancestor common to both H. sapiens sapiens and H. neanderthalensis dates back to about 450,000 years ago. However later analysis showed that Neanderthals had exactly the same version of the FoxP2 gene associated with the use of language, as modern humans — a similarity that would be difficult to explain if the two groups evolved separately. This would mean that Neanderthals not only were our long-ago relatives, but contributed an important part of what it means to be human. In 2009, the newly completed sequence using DNA from bone showed that humans and Neanderthals genomes are 99.5 % similar.

Deoxyribose

5 carbon sugar of DNA nucleotides that lacks an oxygen on the 2' carbon

Ribose

5 carbon sugar of RNA with an OH group on the 2' carbon (compared to deoxyribose of DNA that lacks an oxygen on the 2' carbon

Fossil Records

A fossil is the preserved remains of an organism from a remote past. Whether a plant or an animal, an organism is only fossilized when they are buried by sediment (or volcanic ash) immediately after death. This is a rare process because most organisms are eaten by scavengers or subjected to decay though the rages of time. In addition, most fossils are extremely fragile and easily destroyed through natural phenomena such as earthquakes, tornados, floods, hurricanes, or rigid weather conditions. Further, only a fraction of fossils are located on the Earth's surface. Most fossils are deeply buried beyond the reach of paleontologists, scientists who study prehistoric life forms. -The totality of fossilized artifacts and their placement in rock formations and sedimentary layers.

Gene

A gene is a segment of DNA, and the nucleotides within this one segment of DNA encode one protein. One gene is essentially a series of codons, or you can think of it as several nucleotide words strung together into a sentence. If you translate all of the codons of one gene you would make one protein. 2% of the human genome is composed of genes, which is approximately 30,000 genes. A series of codons within a DNA sequence; also includes regulatory regions of DNA such as a promoter

Genome

A genome is a full set of chromosomes. The human genome is made of 3 billion base pairs that are separated on 23 chromosomes

Segmentation

A long axis, such as the anterior-posterior axis that runs from head to tail, can be further subdivided into segments. Think about the vertebrae in your spinal column - cervical vertebrae are located in your neck, thoracic vertebrae run down the majority of your trunk and have ribs, lumbar vertebrae are in your lower back and sacral vertebrae fuse to form your pelvis (Figure 13). Each of these regions represents a different segment of the vertebral column's anterior-posterior axis and each has a specialized function. The segmentation is exact and precise - all humans have the same number of cervical, thoracic, lumbar and sacral vertebrae. How does the embryo know how many vertebrae to include in each segment? Instructions are provided by the homeobox (Hox) gene family. Hox genes are some of the master regulators of differentiation during embryonic development and we will continue discussing them in the next module.

Causes of DNA Mutation

A mutation in DNA is caused by modifications of one or more nucleotides in the DNA. Mutations can occur during replication, but here we will briefly discuss two ways in which DNA can be damaged from extracellular factors leading to DNA mutations. 1) UV light Ultraviolet light can harm the DNA molecules of living organisms in different ways. In one common damage event, adjacent Thymine bases bond with each other instead of across the "ladder". This makes a bulge, and the distorted DNA molecule does not function properly. 2) Mutagenic chemicals Molecules of a certain size and chemical nature can fit themselves in between base pairs of DNA. Both of these types of changes can affect two important processes; the making of a new copy of a DNA molecule (replication) and the transfer of information from a DNA molecule to an RNA molecule (transcription).

Mimicry

A perfect example of adaptation is mimicry. Mimicry is a common perceived characteristic shared by different groups of organisms that protect one or both groups. A chameleon is a reptile that has the ability to change the color of their skin. Although this change in color is in response to communicate (e.g. mood and mating), or to exposure to light or temperature, chameleons are naturally colored for their surrounding as a camouflage to avoid predators. Other animals can have the ability to blend in to their natural surrounding although they cannot change their skin as chameleons do.

Metastasis

A second feature of cancer is its ability to spread to other tissues. This process is called metastasis. Metastasis has several stages. First, cancer cells from the primary tumor spread to the surrounding tissues. The cancer cells produce digestive enzymes and begin to break down the healthy tissue around the tumor. Eventually, the cancer cells will reach a blood or lymphatic vessel. The cells enter these vessels, facilitating transport throughout the entire body. Many of the cancer cells will die in the blood vessels. The surviving cancer cells may ultimately leave the vessels and take residence in a new tissue, where a secondary tumor may form. -the ability for cancer to spread to other tissues.

Clubbing

A symptom associated with cystic fibrosis where the fingers and toes have a rounded appearace.

Acute Chest Syndrome

A symptom associated with sickle cell anemia where sickle cells get trapped in the lung and cause infection

Hand-foot Disease

A symptom associated with sickle cell anemia where the hands and feet swell due to blockage of vessels by sickled cells

Teratogen

A teratogen is any chemical or environmental factor that can cause birth defects in an embryo. Teratogens include radiation, viruses, alcohol, retinoic acid, and many other drugs. A chemical or environmental factor that causes birth defects in an embryo

Change from Embryo to Fetus

After only eight weeks of development, the embryo has formed all the major organ systems. It has hands, feet, eyes, eyelids and even fingerprints. All of the most dramatic transformations have taken place, and the chance of miscarriage drops sharply. For the remaining 30 weeks of pregnancy, the embryo is called a fetus. During the fetal stage, the organ systems continue to grow and develop, becoming more functional every week. Normal gestation time for human babies is 36-40 weeks post-fertilization. Thanks to incredible advances in medical technologies, more than 50% of premature babies can now survive even if they are born after only 24 weeks of pregnancy. Because the lungs and brain are the last organs to fully develop, many premature babies have immediate problems with breathing, and later problems with cognitive function.

Natural Mutations

Age: Every time a somatic cell passes through the cycle cell, it must replicate its DNA. The human genome is around 3.1 billion nucleotides, each of which is copied individually. Due to the massive amount of replication events that occur, mistakes are bound to occur. The cell checks the accuracy of DNA replication and repairs as many mistakes as it can. Over time, more and more mutations build up, it becomes more difficult to repair them all. For this reason, age is a risk factor for cancer. Tumor Suppressors: it generally requires the mutation of multiple tumor suppressors and at least one oncogene to cause cancer. Some families and even whole populations are born with mutated copies of genes, reducing the number of mutations needed to develop cancer. For example, mutations in the tumor suppressor genes BRCA1 BRCA2 (Breast Cancer) are often inherited, making these individuals more susceptible. In the event of known inherited mutations, it is important to have frequent screening for early detection and to make healthy lifestyle choices to reduce other risk factors.

Alcohol

Alcohol is probably the most devastating teratogen because of how many children it affects. When a mother drinks alcohol during pregnancy, her infant has a chance of developing Fetal Alcohol Syndrome (FAS). Any amount of alcohol at any stage of development can negatively affect the embryo, but the severity of FAS increases proportionally with the amount and duration of alcohol exposure.

Amish & Founders Effect

Amish people in eastern Pennsylvania originated from a small number of German immigrants -- about 200 individuals. They carry unusual concentrations of gene mutations that cause conditions such as Ellis-van Creveld syndrome resulting in short stature and polydactyly (extra fingers or toes). The syndrome is common in the Amish because of the "founder effect."

Disease

An abnormal condition that impairs normal bodily function and is associated with certain symptoms

CFTR channel

Another way to think about this is through a feedback loop. The cell must maintain a balance of chloride ions between the inside and outside of the cell to keep a healthy layer of mucous lining the lungs and digestive tract. The CFTR channel is responsible for maintaining the flow of chloride ions out of the cell, which in turn keeps the intracellular and extracellular chloride ions at equilibrium. Let us take a closer look at how the CFTR channel regulates this balance. On the left side of the figure, the CFTR channel is closed (note the brown, blue, and green structures all make up the channel). In order for the channel to be open, or activated, it must be phosphorylated, which just means an enzyme adds a phosphate group to the channel protein. Phosphorylation is represented by the pink P's in the circles. The channel also requires energy in the form of ATP to actively pump chloride ions outside the cell. When the channel is phosphorylated and ATP binds to the channel, the channel is open, and chloride ions are pumped to the outside of the cell. There is a region inside the pore that senses the chloride concentration outside of the cell, and this sensor will put the activation of the channel into action.

Tumors

As a result of uncontrolled growth, most cancers form tumors, solid lesions formed by abnormal growth of cells (Leukemia, a form of blood or bone marrow cancer, is one exception). Tumors may be either benign or malignant.

Dysplasia

As cancerous cells continue to divide, their appearance gets more and more unhealthy. This is known as dysplasia from the Greek word for malformation. They develop ragged edges and lose their normal pattern of organization. Additionally, cells may develop large, abnormally-shaped nuclei, lose their size uniformity, appear disorganized, have a small amount of cytoplasm relative to the nucleus, and lose cell-type specific features. -from the Greek word malformation. As cancerous cells continue to divide, their appearance gets more and more unhealthy.

Benign Tumors

Benign tumors are self-limited in size, do not invade adjacent tissue, and do not spread throughout the body.

The Tree of Life

Biologists estimate that there are about 5 to 100 million species of organisms living on Earth today. Evidence from morphological, biochemical, and gene sequence data suggests that all organisms on Earth are genetically related, and the genealogical relationships of living things can be represented by a vast evolutionary tree, the tree of life

Cyclins

CDKs are activated after being bound to proteins known as cyclins. The cyclins themselves have no effect on the target proteins, rather they serve to activate the CDKs.

Cancer

Cancer is a disease that will affect nearly all of us in our lifetimes, either directly or through the diagnosis of a friend or family member. Cancer accounts for 1 in 4 deaths in the United States, only heart disease is more deadly. Cancer can occur in people of all ages, though the risk increases with age. While our increased understanding of the biology of cancer has greatly improved physicians ability to treat cancer patients, cancer remains one of the leading causes of death in the United States and worldwide. -Cancer is a group of diseases characterized by uncontrolled cell growth -Radiation therapy and chemotherapy work by causing apoptosis of cancer and normal cells -Risk factors increase the risk that a person will develop cancer -Oncogenes and tumor suppressor genes can promote for protect against disease. Cancer is a category of diseases involving uncontrolled growth and spread of abnormal cells. Cancerous cells have escaped the precise regulatory mechanisms of the cell cycle. This allows cells that would otherwise be deemed unhealthy and thus not be able to divide, to continue to grow without restriction.

HbS

Cause of Sickle-Cell Anemia. The point mutation that occurs in the germ-line DNA hemoglobin beta gene (HBB) is found on chromosome 11. This mutation results in the production of a structurally abnormal hemoglobin (Hb), called HbS. Hb is an oxygen carrying protein that gives red blood cells (RBC) their characteristic color.

Stem Cell Differentiation

Cell communication and tissue specific gene expression is key! Thanks to decades of research, many of the proteins required for differentiation of specific cell types are known. Scientists can bathe stem cells in these proteins, which instruct the cell to differentiate in a certain way. Rigorous tests are performed to make sure the cells display all the expected characteristics of the desired cell type.

Gametes

Cell division is slightly different in germline cells or gametes. These are the sex cells; males produce sperm while females produce eggs, also known as ova. Gametes divide by meiosis.

Cell Growth

Cells are generally quite small. The diameter of the average human cell is around 10 microns. You would need over 2500 cells in a line to measure just 1 inch. Cells do not grow in proportion to our bodies; instead, we produce more cells as we grow. Cell division is our only mechanism of making new cells, thus without cell division, we would not grow taller and wider as we mature, nor would our hair and fingernails grow throughout our life cycle.

Mutations

DNA dictates all aspects of an individual's life and is subjected to changes called mutations. Whether these changes in DNA are beneficial, neutral or harmful to the individual, mutations are random and they occur in the body's cells. Mutations can be heritable only if they happen in reproductive cells and are known as germ-line mutations. Mutations can happen due to intrinsic failures of DNA replication and repair, or extrinsic factors such as chemicals, ultraviolet light and radiation. The bottom-line is that mutations increase the genetic variance within a population. -increases the genetic variance within a population.

Interphase I

DNA is replicated, producing 4n cells

DNA Methylation

DNA methylation is a chemical modification of the DNA molecule itself; it is carried out by an enzyme called DNA methyltransferase (DNMT). Methylation, the addition of a -CH3 group, can directly switch off gene expression by preventing transcription factors from binding to promoters, segments of DNA that promote expression of a particular gene. DNA methylation, or adding a methyl group to the DNA molecule, is like adding a stop light at an intersection. The cars will stop while the red light is there, and the red light can be removed to allow the cars to continue, or the gene to be expressed.

Promoter

Directly before the open reading frame is a promoter region that tells RNA polymerase where to bind. Within the promoter, there is a transcription start site that tells RNA polymerase where to start transcription. Promoters are also used to regulate when a gene is transcribed as well as in which cell type a gene is expressed A portion of a gene found before the open reading frame

Hox Genes

Genes required for patterning the anterior-posterior axis; master regulators of differentiation. They are transcription factors! They help the developing embryo differentiate. When the anterior-posterior axis is relatively undifferentiated, various Hox genes are turned on in specific regions of the anterior-posterior axis. For example, Hox5 is turned on in regions that will form cervical vertebrae, while Hox6 is activated in regions that will become thoracic vertebrae. When Hox5 is present, it acts as a transcription factor and turns on the expression of more genes that will help cells differentiate into cervical vertebrae. Those target genes will then go on to activate more genes, and so on. Transcription factors often act in a cascade, activating increasingly larger numbers of genes that will help a cell acquire tissue-specific proteins, leading to differentiation.

Concepts of Development During Pregnancy

During development, stem cells undergo differentiation to produce specialized cells that perform specific functions. When stem cells divide, they can either produce more of themselves (self-renewal) or can differentiate further. Differentiation is gradual, with stem cells passing through totipotent, pluripotent, multipotent, and unipotent stages before reaching terminal differentiation. Cell differentiation is driven by internal and external factors. Internally, transcription factors (including Hox genes) activate genes at the right time and place. The genes are transcribed into mRNA and translated into tissue-specific proteins. Externally, cells communicate with each other by sending instructional signals that turn on tissue-specific proteins that guide differentiation. Each differentiated cell type expresses a unique set of tissue-specific proteins. Differentiated cells with a common function group together to form tissues, which assemble into organs. This process is called organogenesis. Many organ systems arise due to communication and interaction between cells originating from two different germ layers (e.g. skin forms from ectodermal epidermis and mesodermal dermis). The nervous, circulatory, digestive, and respiratory systems all form from primitive tubular structures. Signals from different mesodermal cell populations help organize anterior-to-posterior differentiation along the length of the tube. The embryonic stage ends at the 8th week of development when all the major organ systems have formed, at which point it is called a fetus for the remainder of the pregnancy. Normal development takes 36-40 weeks.

Implantation

During development, the growing embryo will need a steady supply of nutrients and oxygen, and will need to discard waste materials like carbon dioxide. These needs are met through a constant connection with the bloodstream of the mother via the umbilical cord and placenta. To build this connection, the embryo implants itself into the wall of the mother's uterus. Implantation usually takes place a week or so after fertilization when the embryo is at the late blastocyst stage. The embryo "hatches" from the zona pellucida and the trophoblast cells bind the uterine wall. Enzymes released from the trophoblast break down uterine tissue and the embryo burrows inside (Figure 9). Descendants of the trophoblast grow outward and form the embryonic half of the placenta (the other half comes from the mother). Blood vessels grow into the placenta, forming the umbilical cord that allows exchange of nutrients and gasses. You can still see remnants of this previous connection to your mother - your belly button is a section of the umbilical cord that was tied off at birth! After implantation the blastocyst secretes human chorionic gonadotropin (hCG), the hormone detected by home pregnancy tests and one of the causes of morning sickness.

Phosphate Group

Each nucleotide of DNA or RNA contains a phosphate group on the 5' carbon. This group is important for the formation of DNA or RNA polymer chains from individual nucleotides. The phosphate group on the 5' carbon of one nucleotide can react with the OH group on the 3' carbon of the sugar ring of a different nucleotide to form a bond between two nucleotides to make single stranded DNA or RNA. attached on the 5' carbon of the central sugar of DNA and RNA, it can interact with the 3' carbon of other nucleotides for form a single strand of DNA

Law of Segregation

Each of the two inherited factors (alleles) possessed by the parent will segregate and pass into separate gametes (eggs or sperm) during meiosis, which will each carry only one of the factors. Think back to the description of meiosis in the cell division module. In Meiosis I, sister chromosomes are paired and then separated from each other. Because of this separation, maternal and paternal genes are distributed to different gametes. This process provides the mechanism for the law of segregation.

Telophase I

Each pole now has a haploid set of chromosomes with two sister chromatids each. Cytokinesis generally occurs during this stage.

tRNA

Each tRNA has two specific features that makes them unique: 1) The anti-codon: a three base region within a tRNA which specifically complements a particular nucleotide codon. 2) Amino acid binding site: each type of tRNA can only bind one particular amino acid. Because of these properties, tRNA can interpret and translate the nucleotide language into protein language. The anti-codon recognizes a codon in the mRNA and the amino acid that is attached specifically to that tRNA is added to the growing amino acid chain. A small RNA that transfers a specific amino acid to a growing amino acid chain at the ribosomal site of protein synthesis during translation

Law of Dominance

Each trait is determined by two factors (alleles), inherited one from each parent. These factors each exhibit a characteristic dominant, co-dominant, or recessive expression, and those that are dominant will mask the expression of those that are recessive. Free earlobes are the dominant allele, while attached earlobes are recessive. It is conventional to capitalize the dominant allele and make the recessive allele lowercase. We shall call the free allele "F" and the attached allele "f." You have two copies of this gene, one from each parent. Thus, the possible genotypes are FF, Ff, and ff. Because F is dominant, the presence of one F allele is sufficient to give a free earlobe phenotype. Therefore, individuals with FF or Ff genotypes has the free earlobe phenotype. The recessive allele can only exert its phenotype if it is not masked by the dominant allele, and thus the attached ear phenotype is only observed when an individual's genotype is ff.

Blastomeres

Early embryonic cells at the cleavage stage. Cell division during the cleavage stage generates special embryonic cells called blastomeres. Blastomeres are undifferentiated, meaning that all cells are exactly alike and have not yet become specialized. In fact, this is how identical twins form - blastomeres divide into two separate cell masses. Since all cells are identical, each cell mass has the ability to develop into a complete person. blastomere cell cycles are different than normal cell cycles. A normal cell cycle consists of DNA synthesis (S) and mitosis (M) separated by two Gap phases (G1 and G2) that allow the cell to grow. Blastomeres going through cleavage skip the G1 and G2 phases, so they do not have time to grow in size or double the amount of cytoplasm before dividing into two new cells. The undifferentiated blastomeres of the inner cell mass can be removed and used as embryonic stem cells. At the end of cleavage, blastomeres of the inner cell mass are non-descript and unorganized.

Cleavage

Early embryonic stage characterized by cell division in the absence of cell growth. The 2nd stage of development, called cleavage, lasts nearly one week and is characterized by a rapid and exponential increase in cell number. These are the first signs of differentiation and uterine implantation. Cleavage is known as a period of "cell division in the absence of cell growth". Without cell growth, the total amount of cytoplasm in the embryo does not change, cells get progressively smaller at each division and the developing embryo remains the same size as the original zygote. Cleavage ends with the formation of a hollow ball of cells called the blastocyst. At the end of cleavage, blastomeres of the inner cell mass are non-descript and unorganized. Cell division (Zygotic cell cycle) Cell cycle differences Blastocyst Implantation The newly fertilized embryo undergoes mitotic cell divisions known as cleavage. Cleavage results in an exponential increase in cell number, but the embryo does not grow in size (blastomeres get smaller at each division). The end result of cleavage is a blastocyst, which implants into the uterine wall. Trophoblast descendants form the placenta and establish a physical connection to the mother's blood supply, while the inner cell mass (also known as embryonic stem cells) continues dividing and will give rise to all embryonic tissues.

Epigenetics

Epigenetics is the study of how modifications to DNA or histones, but not to the DNA sequence itself, alter expression of genes. The two major types of epigenetic modifications, methylation and deacetylation, can repress or activate genes, respectively. If all cells in the body have the same exact DNA (except for gametes, of course), then how are they so different and how can they perform such different functions? The answer lies in part in how the expression of genes is controlled. In other words, having the DNA sequence which encodes for a gene does not help you if this gene is not being expressed. And that is what epigenetics means: changes in DNA expression that are not related to the DNA sequence, but rather to the "signals" that allow a gene to be expressed. In order to understand how epigenetic control of gene expression works, we must first review how DNA is "packaged" inside the cell. DNA does not exist as naked molecules in the cell; it is associated with proteins called histones to form a complex substance known as chromatin Epigenetics refers to non DNA factors that influence transcription and translation which is transmitted to new generations. A person who gets skin cancer due to UV radiation but does not pass it on to the next generation is not an example of epigenetics. An obese person whose succeeding offspring have obesity is an example of epigenetics. Some chemical factor associated with obesity is transmitted to succeeding generations. Epigenetics may occur at the histone/DNA junction due to environmental factors or environmental factors may also influence some process of transcription or translation. Keep in mind that the term: environmental factors can be any physical change in DNA caused by chemicals in or around the cells or factors external to animal itself such as sunlight. -the study of how modifications to DNA or histones alter expression of genes that is not related to the DNA sequence.

Niche

Every species is adapted to a selection of environmental properties such as climate and resources (e.g. food and shelter), and they provide an organism with the required living conditions known as a niche.

Stabilizing Selection

Example: When the birth weight is too low babies often have higher risk of infection and high birth weights result in complications at birth. So, in this case, selection works towards stabilizing the average value for the trait birth weight. Until the beginning of the last century this has been true. Today, since we have more C-section delivery averages, this trait value may have changed. -average trait value is going to stay the same.

Fertilization (Sperm and Egg)

Fertilization takes place when specialized cells called gametes fuse together. The genome supplied by each gamete combines together to provide the genetic basis for a new individual.

Start Codon

Following the promoter, the first codon of every gene is always the same, ATG (in the coding strand, so TAC in the non-coding template strand). This is known as the start codon. The first three nucleotides (or codon) of any gene. This codon helps indicate where the ribosome should begin translating an RNA into a protein

Hox Genes and Biology

Gene family that encodes transcription factors required for anterior-posterior differentiation

Gene Flow

Gene flow, also known as migration, describes the process of movement of genes in and out of a population. Gene flow occurs when organisms from one population migrate to another, and its rate varies among different organisms. As you can expect, the gene flow rate for a population of mosquitoes might be drastically higher compared to that of a tree. Genetically modified organisms have the potential to transfer the new genes to their wild relatives, such technologies are controversial. The overall effect of gene flow on evolution is that it increases the genetic variation in a population. -the process of movement of genes in and out of a population.

Gene Therapy

Gene therapy is a technique that attempts to correct the mutated genes responsible for the production of an abnormal protein and the development of a genetic disease. A technique that tries to correct a mutated gene that is responsible for a genetic disease There are mutiple general approaches used to counteract a mutant gene by gene therapy: 1. Introduce a normal (unmutated) copy of the gene to another location in the genome (other than where the gene normally resides in the genome) 2. Swap the abnormal gene with a normal copy of the gene 3. Alter the regulation of the mutated gene Currently gene therapy is only used in clinical trials. This means that scientists and doctors are still in the process of determining the best methods of delivery and gene expression as well as making sure that their therapies do not cause other major side effects in their patients. Despite these challenges, gene therapy is a promising method to offer possible cures for difficult and devastating genetic diseases.

Genes

Genes are segments of DNA. Genes are segments of DNA (Figure). As you learned, DNA is made of a string of four different nucleotides (Adenine, Guanine, Thymine, Cytosine) that can be combined in any order. The nucleotides are transcribed from DNA to RNA. The RNA is organized in nucleotide triplets called codons. Each codon is then translated into a specific amino acid. Proteins are composed of these amino acids. Therefore, genes encode proteins

Evolution and Sickle-Cell Anemia

Genetic diseases are caused by variant genes or chromosomes also known as alleles (one inherited from the mother and another from the father) at one or more genetic loci, which range in frequency from very rare to moderately common. Allele frequencies are the subject of population genetics, which can be readily applied to two tasks: 1. Determining the reasons for the frequency of a deleterious allele 2. Estimating the likelihood that a person will inherit the allele or develop the trait caused by a point mutation and the full-blown disease requires both the gene alleles to be defective (homozygous condition). Since homozygous individuals are highly susceptible to sickle cell anemia, they should be selected against with time. But individuals with sickle-cell anemia are resistant to malaria, highlighting the survival value in carrying the sickle-cell gene within the human population. high frequency of individuals with sickle-cell anemia genes in Western Africa (a range between 10 to 40 %, Fig. 26), compared to other parts of the globe (less than 1 % in South Africa), an observation that intrigued doctors and researchers. In a malaria disease-free environment, a human having defective red blood cells that cause an "unfavorable" anemic condition should be at a great disadvantage to survive, find a mate and reproduce. However, the presence of Plasmodium parasites in sub-Saharan Africa changed the notion of fitness in this environment. Plasmodium parasite infection thrived in individuals with healthy red blood cells, causing disease and death, but the individuals who are carriers of the sickle-cell gene were more resistant to malaria, and had enhanced survival and reproductive success. Yet, this advantage is completely lost when a carrier of the sickle-cell gene moves into a malaria-free region, like the United States, which is why the carrier population is much lower.

Genetic Drift

Genetic drift is a stochastic process based on chance. Basically, genetic drift is the loss of alleles (alternate forms of a gene) in a population. There are two types of effects that genetic drift cause: the "bottleneck effect" & the "founders effect" -a stochastic process based on chance; the loss of alleles in a population.

Genetics

Genetics is the study of how genes bring about characteristics, or traits, in living things and how those traits are passed on from one generation to the next. To put simply, genes are portions of our genetic code (DNA) that make proteins. While each of us generally has the same types of proteins, there may be slight variations from person to person in either how the protein is made or how much of the protein is made. Genetics seeks to explain these variations. Amazingly, while genetics studies how DNA tells our body to make proteins and how these instructions are passed on to our offspring, many of the major concepts of genetics were described before DNA was discovered.

Capacitated

Good timing is essential since the sperm need to be in the female reproductive tract long enough to become activated, or capacitated, but not so long that they die.

Mendel's Theory of Heredity

Gregor Mendel (1822-1884, Fig. 28), an Austrian monk, discovered the laws of heredity in about 1856 - 1863. Mendelism has been the generally accepted theory of heredity since the 1920's and is the basis of all modern genetics. It was destined eventually to allow a revival of Darwin's theory, but its initial effect in the first two decades of the century was the exact opposite. The early Mendelians all opposed Darwin's theory of natural selection. The combination of natural selection and Mendelian genetics gave rise to Neo-Darwinism but only with later support from other scientists work.

Purposes of Cell Division

Growth, Repair of Tissues, Reproduction

Neanderthal Man

H. neandertalensis was somewhat shorter but much more robust than contemporary Homo sapiens. Distinctive cranial features of Neanderthals included prominent brow ridges, low, sloping foreheads, a chinless and heavy, forward-jutting jaw, and extremely large front teeth braincase measured on average about 1600 cm3, larger than contemporary H. sapiens. With their thick, squat build, they are the first hominid to spend extensive times in cold environments in which they lived during the last glacial period. Large front teeth may have reflected a practice common among Eskimo populations of softening animal skins by chewing. Forceful chewing is also suggested by the heavy jaw and brow ridge, both of which serve to buttress powerful muscles. known for having stone tools, being proficient hunters and having aesthetic behaviors and religious beliefs (evidence from burial sites) but they were a highly mobile species. scientists argue that they became extinct and were replaced by modern H. sapiens and others argue that their anatomical distinctions were diluted through gene flow with other H. sapiens.

HBB Gene

Hemoglobin beta gene that is mutated to cause sickle cell anemia

Charles Darwin

His grandfather was a famous scientist and philosopher named Erasmus Darwin, who questioned the idea of species as a fixed entity. boat called "The Beagle". He observed many natural phenomina during this voyage and made collections. He kept a journal of his observations. This became Darwin's first book. It is a great travel book titled "Voyage of The Beagle" (1839). One of his collections during this time were the finches of the Galapagos Islands. These finches were to become known as Darwin's finches Influenced by Charles Lyell and Thomas Malthus

Deacetylation

Histone deacetylation refers to the function of enzymes called histone deacetylases (HDACs), which function to chemically modify histones and change chromatin structure. Chromatin containing acetylated histones is open and accessible to transcription factors, and the genes are potentially active. Histone deacetylation causes the condensation of chromatin, making it inaccessible to transcription factors and the genes are therefore silenced. Certain diseases can also be caused by inappropriate gene silencing. Genes that promote cell cycle progression are often deacetylayted as a mechanism to control their production and thus keep the cell cycle tightly regulated. If one of these compounds acetylates a histone that is associated with one of these genes that is normally silenced, such as a gene called MYC, cancer may result. While deactelyated, MYC is produced at low levels and is generally inaccessible for transcription. Due to its tight chromatin structure, histone acetylation leads to gene expression. Overexpression of a gene that promotes the cell cycle allows the cell to escape the careful regulatory mechanisms in place, thus causing cancer.

Blastocoel

Hollow cavity in the middle of the blastocyst

Modern Man

Homo sapiens started existing about 195,000 years ago. Present day humans evolved with further reduction in the size of molar teeth compared to the early H. sapiens. The average size of the human brain reached 1350 cm3. We made the full transition from hunters and gatherers to a sedentary lifestyle thanks to plant and animal domestication. We developed rich and diverse cultures. After the industrial revolution, we took another step away from nature into an urban lifestyle in the city. No other animal has ever achieved the dominance over nature like human beings have.

Diploid Organisms

Humans are diploid organisms, meaning we have two copies of each chromosome, one inherited from our mother and one from our father. Each gene can be found at a specific place on a chromosome, thus we have two copies of each gene. While each gene encodes for the same protein, there may be differences in this protein based on the genetic variation between individuals.

Domestication and Breeding Versus Monocultures and Pesticides

Humans used to have small and diverse crops with high genetic diversity that protected the crops from major plagues where the disease of one crop did not compromise the others. The monocultures that are the norm today are a big incentive for a few species of insects, which now have abundant food and a death sentence for others which relied on different food sources. This was a man-made selection where reduced diversity and providing unlimited food to one type of insect facilitated survival of insect pests but compromised the crop resistance. The same is true for pathogenic diseases and the potato crop failure and the Great Irish Famine, which lost a million lives in Ireland and resulted in mass migration. The answers to this rely on understanding evolutionary principles and increasing the genetic diversity of our crops. In developing pest and disease resistance for animals and plants, we only take another step in the cycle of selection and resistance. Regardless of how good our breeding programs are, maintaining diversity is an essential task for our survival.

Surgery

If a cancer has not metastasized and the tumor is accessible, surgery may be sufficient to eradicate the cancer. Early detection is key, the longer cancer has been present, the greater chance that it has spread through the body. It's easy to find and remove cancer when all the cells are grouped in a tumor.

Homologous

If all life forms on earth share a common ancestor, then evolution predicts that related organisms will have similar characteristics, or homologies. Comparative anatomists dedicate their entire careers to investigating evolutionary relationships in bone structures. Homologous anatomical structures are those that evolved from the same structure in a common ancestor. homologies can be established for the functions of different organs, in the development of embryos, or behaviors among different types of living forms. ex: human's arm is used to grasp, a horse's foreleg to walk, a whale's flipper to swim, and a bat's wing to fly, the bones are homologous to each other because they share the same physical and functional characteristics within the overall structure of a forelimb -anatomical structures that have evolved from the same structure in a current ancestor. These structures share the same physical and functional characteristics.

Homozygous

If both of your alleles are identical, you are said to be homozygous (Greek: homo = same, zygous = paired) -both alleles are identical.

Meiosis

If gametes were created by mitosis, each would be diploid (two complete sets of chromosomes) and the fusion of two gametes would yield 4 sets of chromosomes. If this were the case, the number of chromosomes would double with each generation. This would be incompatible with life. Therefore, a different process of cell division called meiosis (Greek "meio" = less) is used to generate gametes. The male gamete is sperm, and the female gamete is the egg (Figure 15), these cells are produced exclusively in the testes and ovaries, respectively, by the process of meiosis. Meiosis shares many steps with mitosis, but the end result is different. While mitosis generates diploid cells (2n), meiosis results in haploid cells (n). Meiosis includes one DNA replication and two separate cell divisions, meiosis I and meiosis II. Like mitosis, each cell division of meiosis consists of prophase, metaphase, anaphase, and telephase

Macroevolution

If given enough time, small changes can produce character changes that result in major evolutionary changes or macroevolution. Macroevolution is defined as descent with modification of groups above the species level (at a large scale). For example, instead of looking at genetic changes with the human species, macroevolution encompasses changes at the primate, mammal, or vertebrate levels. It is an analysis of evolution in separated gene pools. -decent with modification of groups above the species level or at a large scale.

Discontinuity (Distribution Patterns)

If one takes into account that evolution is continuous through time and space, together with Earth's continental drift, then one can predict that North America should be the link between these the two isolated areas where the camel family is found. However, we all know that there are no camels in North America. The proof for this prediction came with the discovery in North America of a large fossil fauna of Tertiary camels. Based on the age of this fossil record, the llamas may have originated from the central plains of North America about 40 million year ago and migrated to South America and Asia about 3 million years ago. In addition, it appears that camels became extinct in North America by the end of the last ice age (10,000-12,000 years ago)

Zona Pellucida

If sperm are able to pass through the first barrier, they next try to attach to the zona pellucida, the tough coating surrounding the egg. Protective barrier surrounding the egg; contains species-specific recognition proteins. If sperm binding is successful, the acrosome releases enzymes that chew a hole through the zona pellucida.

Sperm Fusion

If sperm binding is successful, the acrosome releases enzymes that chew a hole through the zona pellucida. The hole allows the sperm to contact the plasma membrane of the egg. Fusion of the plasma membranes allows the sperm nucleus to enter the egg, creating a single-celled embryo called a zygote. The zygote is diploid (2N) since it results from the fusion of two haploid (1N) gametes. Fertilization releases the egg from its suspended state, triggering production of new proteins and initiation of the cell cycle (mitosis).

Heterozygous

If the alleles differ from each other, then you are known to be heterozygous (Greek: hetero = different). -the alleles differ from each other.

Punnet Square

If the genotypes of both parents are known, it is possible to determine the potential genotypes of the offspring. This is accomplished by the use of a Punnett Square. A Punnett square is a diagram that provides a summary of every potential allele combination that would result in offspring. In it's simplest form, it is a 2 X 2 square with the maternal and paternal genotype listed outside the box (Figure 1). You simply transfer the parental alleles to the boxes below or to the right of them. The resulting four new combinations of alleles are the potential genotypes of any offspring. In this example, two heterozygous parents (Bb) mate, which can yield offspring that are either homozygous dominant (BB), heterozygous (Bb), or homozygous recessive (bb). There is a 25% chance of BB, 50% chance of Bb, and 25% of bb. These are known as simple mendelian ratios.

Undifferentiated Cell

Immature cell that has not yet acquired special structure or function; for example a stem cell.

Gregor Mendel

In 1866, Gregor Mendel studied the transmission of seven different pea traits by carefully test-crossing many distinct varieties of peas. He spent an enormous amount of time crossing different types of these plants and carefully observing and documenting the results. His observations led to a great understanding of how genes are passed on from generation to generation.

Australopithecus afarensis (Lucy)

In 1974 a team of scientists led by Donald Johanson uncovered the fossil remains of a creature who fell to her death 3.2 million years ago. Lucy was a 25 year old female Australopithecus afarensis who was about 3'6" tall and weighing 62 lbs. Lucy was discovered in Hadar, Ethiopia. the pelvic and leg bones are arranged for bipedal locomotion similar to modern humans. The ratio between arms and legs of Lucy is 84.6 (whereas that of men is about 71.8 and of chimpanzees 100). They were also more human-like in that their canine teeth were smaller than those of apes, their brain size expected to be 375 to 550cc, and the jaw angles intermediate between the rectangular shape of chimpanzees and the parabolic of humans. This evidence suggests that A. afarensis is the most ancient common ancestor from which all other hominids sprang and A. afarensis are the intermediate species between apes and humans. Lucy's broad fan shaped hip bones are similar to a modern human woman's hip bones and can support internal organs and the entire upper body that is needed in an upright position.

Phosphorylation

In most cases, phosphorylation serves to activate the target protein.

Convergent Evolution

In some cases, separate evolutionary lineages evolved similar features that are the result of common environments rather than common ancestry. This is called convergent evolution.

Law of Independent Assortment

In the gametes, alleles of one gene separate independently of those of another gene, and thus all possible combinations of alleles are equally probable. Again, think back to what you learned about meioisis. During Meiosis I, the process of homologous recombination occurs. This makes it so that genes that are on the same chromosome do not necessarily end up in the same gamete. Without homologous recombination, each chromosome would be passed down as it was received from your mother or father. Instead, new gene combinations are made that combine alleles from each parent. Thus, homologous recombination provides the mechanisms for law of independent assortment.

Epigenetic Carcinogens

In the last module we discussed how carcinogens can mutate your DNA, which can lead to the development of cancer. Some carcinogens can cause cancer without mutating DNA, these are known as epigenetic carcinogens. Examples of epigenetic carcinogens include hexochlorobeneze (fungicide), diethylstilbestrol (synthetic estogren), arsenite, and nickel compounds.

Differential Survival and Reproduction

Individuals possessing traits well suited for the struggle for local resources or environment will contribute more offspring to the next generation.

In Vitro Fertilization

Infertility treatment where an embryo is created by combining egg and sperm in a petri dish

3 Main Steps in Transcription

Initiation, Elongation, and Termination

Interphase

Interphase is the part of the cell cycle when the cell grows by synthesizing proteins, cytoplasmic organelles, and DNA. -G1, S, G2

High Rate of Population Growth

Most populations have more offspring each year than local resources can support. That results in a struggle for resources. Therefore each generation may experience substantial mortality. In other words, every generation produces more offspring than can survive.

Tumor Suppressor Genes

Just like in a car, the cell cycle has brakes to counteract the accelerator. These mechanisms tell the cell cycle to "stop." In biological terms, these proteins are made by tumor suppressor genes. If these genes mutate, the cell does not receive signals to stop. To continue with the car analogy, it is as if someone has cut the brake line,disabling them. This is also a very common mechanism of cancer development. Nearly 60% of all cancers involve a mutation in a tumor suppressor gene called p53. -the process in which genes that send out a "stop" signal become mutated and the cell does not receive signals to stop.

Meiotic Nondisjunction

Like all biological processes, meiosis does not always function as it should. In some meiotic events, the chromosomes do not properly separate from each other. This is called meiotic nondisjunction. Meiotic nondisjunction can occur during either Meiosis I or Meiosis II. If it occurs during Meiosis I, all gametes will be affecting having either too many or too few chromosomes. If it occurs during Meiosis II only 2 out of the 4 gametes produced will be abnormal. If a disjunction event occurs during gamete development, the resulting offspring will more than likely be abnormal.

Phylogeny

Lineage-splitting (or speciation) can be identified by constructing and examining a phylogeny. The phylogeny might reveal that a particular lineage has undergone unusually frequent lineage-splitting or low rate of lineage-splitting or it might reveal that several lineages experienced a burst of lineage-splitting at the same time

Character Change

Lineages can change quickly or slowly by changing characteristics. Trilobites, animals in the same clade as modern insects and crustaceans, lived over 300 million years ago. As shown below, their fossil record clearly suggests that several lineages underwent similar increases in segment number over the course of millions of years. Lineage-splitting (or speciation) can be identified by constructing and examining a phylogeny.

Chromosomes

Long double strands of DNA are wrapped around proteins to form chromosomes, and this packaging of DNA allows all of the DNA to fit within a single cell. long strands of double stranded DNA packaged around proteins.

Malignant

Malignant tumors grow uncontrollably, invade adjacent tissues, and spread throughout the body. Only malignant tumors are considered to be cancerous.

Vegetables from Wild Mustard

Many of the artificially developed vegetables and domesticated animals are good examples of macroevolution. For example, human farmers cultivated wild mustard to select for desired traits such as larger leaves, buds, and flowers. Many common vegetables are cultivated forms of wild mustard.

Mendel's Principles of Genetic Inheritance

Mendel's observations led him to create three rules regarding how our traits are passed on from generation to generation. Mendel's principles are: law of segregation, law of independent assortment, law of dominance. These three laws have provided the fundamental basis for our understanding of genetics. Our current knowledge of the molecular basis for genetics has led us to understand that inheritance is far more complicated than it was initially described by Mendel. Nonetheless, Mendel's laws generally hold true to this day.

Mendel's Law

Mendel's simple approach led to fundamental insights into how genes are inherited, known today as Mendel's Laws. At the time, the molecular mechanisms behind these laws of inheritance were completely unknown. Nonetheless, Mendel demonstrated his understanding of the principles of genetics by correctly predicting the behavior of traits and how they are transmitted. From his experiments in breeding garden peas, Mendel developed three major underlying principles of genetics.

Discontinuity (Fossil Records and Biogeography)

Mesosaurus was significant in providing evidence for the theory of continental drift (movements of continental plates around the world), because its remains were found in southern Africa and eastern South America, two far away places. As Mesosaurus was a freshwater animal, and therefore could not have crossed the Atlantic Ocean, this distribution indicates that the two continents used to be joined together

Microevolution

Microevolution represents change in gene frequency within a population of a small scale. This change introduced the sickle-cell gene within a human population that resulted in a favorable or unfavorable trait depending on a given environment. Yet, this change was not enough to create a new humanoid species. Mutation, migration and genetic drift are mechanisms that create microevolution. -change in gene frequency within a population of a small scale.

House Sparrows in the United States

Microevolution: The house sparrows were introduced to North America in 1852. Since then, the northern house sparrow populations are larger-bodied compared to those in the south. Natural selection has acted on the original house sparrow population and resulted in larger-bodied birds that can survive lower temperatures in the north and smaller-bodied birds in the south. Physiologically larger body size is an advantage to survive the northern cold winters.

Prophase II

Microtubules form

Evolutionary Body Plan

Most animals that share a common evolutionary history tend to look very similar during early development. Features that make the animals unique, such as hair, feathers, or scales, emerge at later developmental stages. These observations have led scientists to hypothesize that similarities between early embryonic body plans are reminiscent of the body plan of a common ancestor, while unique characteristics that appeared after species diverged do not appear until later in development. Basically, what makes us "human" does not necessarily become evident until later in development. Until then, we are hard to distinguish from other animal species.

Reproduction

Most cells have two copies of each chromosome. If these cells combine, the resulting cells would have four copies of each chromosome. The number of chromosomes would double each generation! Instead, a specialized process of cell division called meiosis takes place in gametes (sperm and eggs) to prevent this from happening. This process also contains a critical step that increases genetic diversity in offspring

Habitat Tracking

Most commonly when the habitat or climate changes, the populations can move to a more suitable habitat. This is called habitat tracking.

Adult Stem Cells

Multipotent or unipotent stem cells isolated from adult organs While ES cells hold the most promise in terms of differentiation potential, quite a bit of progress has already been made with adult stem cells. Adult stem cells are generated from multipotent cells in organs, such as hematopoietic stem cells from bone marrow or cardiac stem cells from the heart. Most adult organs contain multipotent stem cells to help replace differentiated cells that are old, injured, or dying. They are hard to isolate and are extremely rare, with less than 1 stem cell for every 1000 differentiated cells. But when they are isolated, they can be very useful. For example, neural stem cells can be differentiated into dopaminergic neurons, which could potentially be used to treat Parkinson's patients. The use of adult stem cells is of great interest to stem cell researchers because it helps avoid the controversies surrounding ES cells.

Differentiated Cells

Muscle-specific myosin is not found in skin cells, while antimicrobial proteins aren't present in muscle cells. Each differentiated cell type expresses a unique combination of proteins that allows it to carry out its specific function. Tissue-specific proteins are the basis of differentiation! all cells in our body contain the exact same DNA sequence since they all derive from the same original cell (the zygote). Since differences do not lie at the level of DNA, they must occur at the mRNA level. This is precisely what happens - differentiated cells arise because tissue-specific mRNAs are expressed (which are translated into proteins). When a cell differentiates, transcription factors turn on genes that are required for that cell to function properly. For example, a muscle cell forms when a gene like myosin is turned on by muscle-specific transcription factors, while genes required for brain cell function will be turned off in muscle cells. The feedback loop to the left shows how cell differentiation is a negative feedback loop.

Germ-line Mutations

Mutations can be heritable only if they happen in reproductive cells and are known as germ-line mutations. Germ-line mutations can have a range of effects on the individual's phenotype from non-detectable to lethal.

Fetus

Name given to a developing human from 8 weeks post-fertilization until birth

Embryo

Name given to a developing organism; in humans the embryonic stage lasts from fertilization through the first 8 weeks of development

p53 Gene

Nearly 60% of all cancers involve a mutation in a tumor suppressor gene called p53. In many cancers, the p53 gene is defective, but p53 is needed for efficient induction of apoptosis in response to DNA damage. Thus, for those cancers caused by cells with defective p53, chemotherapy and radiation therapy may be less effective than for other cancers. Indeed, examining the p53 gene in a particular cancer can help physicians decide on appropriate courses of therapy.

Neurulation

Neurulation begins when the notochord (a mesodermal structure) sends signals to ectodermal cells above it, telling them to form the neural plate. The neural plate is a strip of stem cells that runs down the entire back of the embryo. The neural plate folds in on itself, pinching off to form the neural tube. The upper (anterior) section of the neural tube will differentiate into the brain, while the lower (more posterior) sections will form the spinal cord. Hox genes are turned on during differentiation of the anterior neural tube

Uracil

Nitrogenous base with one ring that is found in RNAs instead of Thymine

Sperm-Egg Binding

Of the 250 million sperm that begin the race to the egg, only 200 sperm successfully make the journey. After the handful of lucky sperm make it to the egg, they still have to breach the two barriers surrounding the egg. The cumulus layer acts as a first line of defense. It lets capacitated sperm through, but holds back inactivated sperm. If sperm are able to pass through the first barrier, they next try to attach to the zona pellucida, the tough coating surrounding the egg. Evolution has created many safeguards to make sure successful reproduction only occurs between males and females of the same species (there is a reason that centaurs and mermaids are mythological creatures!). One of these safeguards is sperm-egg binding, which works much like a lock and key system. The egg can only be "unlocked" if the sperm displays a species-specific protein on its surface (the "key"), which recognizes a species-specific protein on the zona pellucida (the "lock"). If the key does not match the lock, fertilization will not happen.

Chemotherapy and Radiation Therapy

Once cancer has begun to metastasize, physical removal of all cancerous cells is impossible. Instead, chemotherapy and radiation therapy may also be required.

Translation

Once in the cytoplasm, mRNA is ready to convert the DNA language into protein language (amino acids) through a process called translation. Translation uses two other types of RNA, ribosomal RNA (rRNA) and transfer RNA (tRNA). rRNA along with oproteins make up the ribosome, the site of translation. tRNA acts as the interpreter reading the codons of mRNA and translating them into the amino acid language to make proteins. tRNAs bind their specific amino acid from the cell's pool of free amino acids in the cytoplasm and brings the amino acid to the ribosome to be added to the growing amino acid chain. 1) mRNA binds the ribosome. 2) The ribosome scans the mRNA until it finds the "AUG" start codon. 3) The tRNA with the corresponding "UAC" anti-codon binds to the AUG start codon in the mRNA. -This tRNA brings with it the amino acid methionine (Met). The first amino acid of every protein is always methion. 4) The second codon of the mRNA is recognized by the tRNA with the corresponding anti-codon. -This tRNA brings along its specific amino acid. 5) The ribosome begins to build the protein by adding the methionine from the first tRNA to the amino acid on the second tRNA. This pair of amino acids is now attached to the second tRNA. 6) The ribosome moves three nucleotides down the mRNA to the next codon. 7) The first tRNA leaves the ribosome to pick up another amino acid. 8) The third codon of the mRNA is recognized by the tRNA with the corresponding anti-codon. This tRNA brings along its specific amino acid. 9) The ribosome begins to build the protein by adding the two amino acids from the second tRNA to the amino acid on the third tRNA. Thus all three amino acids are now attached to the third tRNA. 10) This process continues until the ribosome reaches one of the three stop codons. There are no tRNAs with an anti-codon to the stop codons. Thus these codons efficiently stop the process of making a new protein and synthesis of the new protein is complete. 11) The newly synthesized protein is released from the ribosome to go off and perform its function in the cell. Translation is complete. The process by which the ribosome uses tRNAs to make a protein from an mRNA by translating the nucleotide codons into amino acids

Nature vs. Nurture

One interesting example of this suggests that a mother's behavior can affect the chemistry of DNA in her offspring. It is often stated that children need parental love and nurturing for successful development as people. In a research study, scientists showed that maternal care was correlated with methylation of the gene encoding the glucocorticoid receptor. Glucocorticoids are stress hormones produced by the body. In order to feel the effects of the hormones, a receptor is needed. Once a sufficient amount of hormone is bound to the receptor, the brain sends signals to shut down the glucocorticoid production, thus ending the stress response. Rats that received more parental care had more stress hormone receptors, and thus were better at responding to stress, leaving them relaxed. In contrast, poorly-nurtured rats had methylated glucocorticoid receptor genes, leaving them capable to responding to stress, thus making them anxious. Many factors can reverse epigenetic modifications, so these effects are not necessarily permanent. Despite their reversibility, epigenetic changes can be passed on to offspring.

Extinction

One of the most important modes of macroevolution is extinction. Extinction can be defined as the cessation of life for a single species or entire taxa. Consider this: over 99.9 % of the species that have ever lived on this planet have gone extinct! Perhaps the most popular mass extinction is that of non-avian dinosaurs that occurred about 65.5 million years ago. Earth has undergone five mass extinctions. In the last two hundred years we changed our habitat drastically

Galapagos Finches and Variation

P. & G. Grant demonstrated that variation exists in Geospiza fortis finches. Among the population there were 751 birds and these birds varied in how big their bill was. This would be a roughly normal distribution. We would get the same distribution if we graphed human height within a population.

Pathogenic Diseases and Evolution of Drug Resistance

Pathogens may be expected to adapt to consistent, strong selection, such as that created by widespread, intense use of therapeutic drugs. Resistance to antimicrobial drugs has evolved in HIV, the tuberculosis bacterium, the malarial protozoan, and many other disease-carrying organisms, rendering previously effective therapeutic controls ineffective. Many of these organisms are resistant to drugs partly because antibiotic resistance genes are often transferred between species of bacteria. H1N1 virus also has gained resistance to Tamiflu required us to find new drugs. The evolution of drug resistance has greatly increased the cost of therapy, increased morbidity and mortality, and has raised fears that many infectious diseases will be entirely un-treatable in the near future. Evolutionary theory suggests that such a grim future may be averted by reducing selection for antibiotic resistance, and the World Health Organization has indeed recommended more judicious, sparing use of antibiotics. The full course of antibiotics have to be used in order to prevent resistant varieties from having reproductive success and carrying on the resistant genes to the next generation.

Diet and Exercise

People who have a poor diet, do not get enough physical activity, or are overweight are at risk for certain types of cancer. It is thought that cancer protective diets include many fruits and vegetables, whole grains, and some proteins (meats, beans, etc.), while avoiding fatty foods and processed meats.

Angiogenesis

Physical properties can limit the size of tumors. If a tumor grows too large, the cells on the inside will not get enough oxygen or nutrients and will die. This begins to happen when tumor diameter is around 1-2 mm. To escape this phenomenon, cancerous tumors produce signals causing blood vessels to grow into the tumor, providing oxygen and nutrients for its cells to continue their uncontrolled growth. This is a process known as angiogenesis (Greek: angio = blood vessel, genesis = origin or beginning), that is a natural part of growth and healing, but has been co-opted by cancer. -cancerous tumors produce signals causing blood vessels to grow into the tumor, providing oxygen and nutrients for its cells to continue their uncontrolled growth. This is a natural part of growth and healing, but has been co-opted by cancer.

Ploidy

Ploidy refers to the number of sets of chromosomes in a cell. Humans have 23 chromosomes. These exist in a haploid state in gametes (top), meaning each cell has one copy of each chromosome. In contrast, somatic cells are diploid (bottom), with 2 copies of each chromosome, for a total of 46.

Induced Pluripotent Stem Cells (iPS cells)

Pluripotent stem cells created by reversing differentiation of a non-pluripotent cell; virtually identical to embryonic stem cells; circumvents the need to destroy embryos The newest fad in stem cell research is induced pluripotent stem cells (iPS cells). Since ES cells are surrounded by controversy and adult stem cells are difficult to isolate, researchers wanted to find a way to get the best of both worlds - cells with unlimited potential that are easy to isolate and avoid ethical problems. This was accomplished in late 2007 when two different research groups transformed skin cells into pluripotent stem cells. This amazing feat was accomplished by turning on the expression of four transcription factors commonly present in ES cells, causing the skin cell to revert back to its original undifferentiated state. iPS cells are nearly identical to ES cells, and no embryos are destroyed in the process.

Viruses

The most common vector used in gene therapy are disabled viruses. The viruses used are modified so they cannot cause disease when used in people. Viruses are used because they have a unique ability to recognize certain cells and insert genetic material into them. You can think of the virus as a molecular delivery truck which unloads its DNA cargo (the normal copy of the gene) into the cell

Embryonic Stem Cells

Pluripotent stem cells isolated from the inner cell mass of the blastocyst. Human embryonic stem cells (ES cells) have traditionally been considered the gold standard for stem cell research because they have the greatest potential to form virtually every cell type. However, they also generate the greatest controversy since creation of new ES cell lines requires that an embryo be destroyed to harvest the inner cell mass (Figure 8). On one hand, pro-life advocates say this constitutes abortion since a human life is destroyed, and therefore the practice is unethical. On the other hand, ES cell advocates say blastocyst-stage embryos cannot be considered true humans yet because they have not differentiated and are not able to survive without being implanted into a womb. There are currently 400,000 embryos being stored at in vitro fertilization clinics around the country, with 12,000 of these scheduled for destruction. Rather than destroying the embryos, should they be donated to stem cell research? In 2001, President Bush allowed the use of federal taxpayer money to fund stem cell research for the first time, with the stipulation that research was limited to existing ES cells lines. The money would not fund creation of new ES cell lines, nor research using ES cell lines created after 2001 with private funding, since he believes in the sanctity of human life. In response, California passed Prop 71 in 2004, providing $3 billion for ES cell research that was not eligible for federal funding. This has made California one of the leading centers for stem cell research. In more recent news, the Obama administration has reversed some, but not all, of Bush's limitations on stem cell research.

Proteins

Proteins are the molecules that perform the functional form of the information. The functional form of cellular information encoded by DNA.

RNA

RNA is the molecule that acts as a messenger carrying the information from DNA to protein. Messenger RNA, known as mRNA, is a mobile short-term storage of cellular information. short for Ribonucleic acid, it is a polymer of nucleotides that acts as a messenger between DNA and proteins

rRNA (ribosomal RNA)

RNA molecule that makes up the ribosome

Types of Cloning

Reproductive Cloning, Therapeutic Cloning, Stem Cell Research

Retinoid Acid/ Vitamin A/ Accutane

Retinoic acid is an interesting teratogen - it is required in small doses for normal development, but in high doses can cause facial deformities, including cleft palate. Retinoic acid is a form of vitamin A, which explains why women are warned to limit vitamin A intake during pregnancy. The normal function of retinoic acid is to activate Hox genes, which as we learned earlier, are essential for setting up the anterior-posterior axis of the embryo. Scientists believe some birth defects caused by excess retinoic acid are due to improper expression of Hox genes at times or places they would not normally be activated. Isotretinoin, the active ingredient in the acne drug Accutane, is also a vitamin A derivative. Women should be especially careful to prevent pregnancy if they are taking Accutane. Retinoic Acid: Vitamin A derivative required in small doses for anterior-posterior patterning in the embryo; activates transcription of Hox genes; acts as a teratogen in large doses Accutane: Treatment for severe acne that acts as a teratogen; active ingredient is a vitamin A derivative

Terminator

Shortly after the stop codon is the terminator region that tells RNA polymerase to stop transcription. A portion of a gene after the open reading frame that signals the end of transcription

Telophase II

Sister chromatids are localized to opposite poles, cytokinesis usually occurs. There are now 4 haploid cells with unreplicated chromosomes.

Prophase I

Sister chromosomes pair together through a process unique to Prophase I called synapsis. At various places along the chromosomes, the chromatids from sister chromosomes exchange DNA with each other at X-shaped structures called chiasmata (singular: chiasma). At these chiasmata, portions of the sister chromatids are exchanged with each other by a process known as crossing over or homologous recombination. If homologous recombination did not occur, each gamete would contain 23 chromosomes, some of which would be exact copies of those you received from your mother, and others exact copies of those you inherited from your father. The process of homologous recombination produces new gene combinations, creating unique chromosomes. Each meiotic cycle may result in different recombination events, thus producing unique gametes. For this reason, homologous recombination is essential for generating population diversity.

Somatic Cells

Somatic cells are cells of the body (non sex cells).

Oncogenes

Some genes involved in cell cycle regulation send a "Go"signal for the cell cycle to proceed when a series of conditions have been met. If these genes mutate, they can change to send a "go" signal regardless of the conditions. When this occurs, the genes become known as oncogenes (Greek: "on co" = tumor). By analogy, these signals are the gas pedal of the cell cycle. It should only be pressed when the traffic light turns green, but in the case of mutation to an oncogene,the gas pedal is stuck to the floor. The mechanism of cancer development is quite common, nearly 30% of human cancers have an oncogenic mutation in a gene named ras. -the process in which certain genes that send out a "go" signal become mutated and the "go" signal is turned even when it is not suppose to.

Coevolution

Sometimes selective forces act upon two different species to reciprocally affect each other's evolution. This phenomenon is known as coevolution and it is mainly present in species that have close ecological relationships with one another. -selective forces act upon two different species to reciprocally affect each other's evolution.

Organogenesis

Soon after gastrulation, cells continue to migrate and rearrange, signaling the beginning of organogenesis. First, cells become specialized by acquiring characteristics that set them apart from other cells, a process called differentiation. Differentiation is a gradual process where cell function becomes more and more restricted over time. Next, related cells group together to form a tissue that carries out a specific function. Finally, different tissues assemble into a working unit called an organ The purpose of differentiation is to generate specialized cells that can group together to form tissues. Different tissues combine to form organs. Interestingly, many organ systems form by combining tissues derived from two separate germ layers. For instance, your skin is made up of the outer epidermis (derived from ectoderm) and inner dermis (derived from mesoderm) layers. The lining of the digestive system derives from endoderm, but the muscles required for peristalsis come from mesoderm. Oftentimes there is direct communication between ectoderm cells and mesoderm cells, or between mesoderm cells and endoderm cells. Signals sent back and forth help cells identify where they are in the body and are essential for proper differentiation.

Capacitation

Sperm activation within in the female reproductive tract

Gastrulation

Stage of embryonic development following cleavage, hallmarked by movement of cells through the primitive streak to establish the three germ layers. At the end of cleavage, blastomeres of the inner cell mass are non-descript and unorganized. During gastrulation, a rough body plan starts to emerge. Dynamic cell movements set up the inner and outer layers of the embryo, along with the body axes. During gastrulation, the inner cell mass rearranges into three germ layers that will form the outside, middle, and inside layers of the embryo. Movement of cells during gastrulation is similar to what happens if you push your finger into an inflated balloon - the cells migrate downward into the embryo (Figure 10). The first cells to move inward form the most internal layer of the embryo, the endoderm. The next group of cells to move inward, the mesoderm, situate themselves on top of the endoderm but underneath the outer layer, forming the middle cell layer. The cells that remain on top of the embryonic disc will form the outer layer of cells, the ectoderm. Each of the germ layers will form different tissues and organs later in development. The inner cell mass begins to organize and take shape. Cells undergo gastrulation and rearrange into three germ layers (endoderm, mesoderm and ectoderm). The three body axes are established - anterior-posterior, dorsal-ventral, and left-right. Further subdivision of the axes is accomplished through segmentation, a process regulated by masters of differentiation - the Hox genes.

Stem Cells and Potency

Stem cells are the foundation of embryonic development for two important reasons: (1) they can replenish themselves in a process called self-renewal that guarantees a continual population of stem cells and (2) they can divide to form subsets of cells able to differentiate. This balance between maintenance of non-committed cells and formation of specialized cells drives development forward. As the embryo develops, stem cells become more and more restricted in their ability to form different cell types.

How Stem Cells Are Isolated

Stem cells have been isolated from three main sources: (1) pluripotent stem cells from the blastocyst inner cell mass (a.k.a. embryonic stem cells), (2) multipotent stem cells from adult organs, and (3) skin cells that were de-differentiated to resemble embryonic stem cells.

Stem Cell Research

Stem cells hold great potential for treating Parkinson's, Alzheimer's, diabetes, and heart disease, or in reversing paralysis due to spinal cord injury. They are also incredibly useful as general research tools (Figure 7). However, many challenges face stem cell research, including how to obtain stem cells, how to get them to differentiate, whether they are actually capable of treating disease, and whether it is ethically responsible to pursue this line of research. Stem Cells are undifferentiated cells that have the ability to form many cell types.

Causes of DNA Mutations

Substitution, Insertion/Deletion, Frameshifts

DNA vs. RNA Makeup

The major difference between a DNA nucleotide and an RNA nucleotide is the group attached to the 2' carbon of the sugar ring (see Figure 1). In an RNA nucleotide the sugar is called Ribose and has an OH group on its 2' carbon, while in DNA the sugar is called Deoxyribose and the 2' carbon only has a hydrogen (H). Thus the sugar is called "deoxy", because it is missing that oxygen (O).

Thalidomide

Thalidomide is a perfect example of why pharmaceutical drugs should be thoroughly tested by the Food and Drug Administration (FDA) before entering the market. Fifty years ago, thalidomide was prescribed to pregnant women around the world to prevent morning sickness and as a sleep aid. Sadly, the devastating effects of thalidomide on embryonic development were not realized until 10,000 children were born with missing or deformed arms and legs. Fortunately, the impact on the United States was minimized thanks to an observant FDA reviewer who prevented the distribution of thalidomide in the U.S., saying it needed more testing. Soon after, Congress passed laws requiring that drugs be tested during pregnancy before being approved by the FDA.

Gap 1 (G1)

The G1 or first gap marks the beginning of interphase. During G1, the cell begins to grow. Many enzymes are made that are needed for DNA synthesis. During this phase, each chromosome exists as a single, unpaired chromatid. Cells that are not currently dividing are most likely to pause the cell cycle during the G1 phase.

Gap 2 (G2)

The G2 or second gap is the final portion of interphase. Cells continue to grow and make proteins. Importantly, microtubules are synthesized during this phase, which are necessary for mitosis.

Galapagos Islands

The Galapagos islands are a chain of volcanic islands west of Peru. There are only a few species of birds in these islands which look similar to each other, but they vary in bill size. They look all relatively the same otherwise, with brown and black feathers and similar body size.

Inducer

The INDUCER senses signals from the environment or the cell. An inducer could be a protein or it could be an energy source like glucose or lactose. The INDUCER senses the environment and binds to the ACTIVATOR.

Activator

The INDUCER senses the environment and binds to the ACTIVATOR. When the INDUCER and ACTIVATOR are bound together, they bind to a region of the promoter called the operator and signal that transcription should start.

Differences in Cro-Magnon Man & Neanderthal Man

The Neanderthal has a pronounced bun shape on the back of its skull, known as an occipital bun, and the forehead and the top of the head are much lower and wider. Cro-Magnon do not have this occipital bun and the forehead and top of the head are much higher and narrower. Their cranial capacities were up to 1590 cm3, which is relatively large even for people today. Neanderthal had a short robust body shape, while Cro-Magnon had a body shape much more like modern people who are adapted to hot climates, tall with long arms and legs. Neanderthal showed many signs of "higher" culture such as burying their dead and caring for their sick, and in the later stages of their existence maybe even created items such as necklaces and jewelry. These characteristics are much clearer in Cro-Magnon. Cro-Magnon culture was far more developed, probably not unlike that of modern hunter-gatherers. Cro-Magnon are also known to build communal shelters unlike the Neanderthal. Neanderthal had no cave art (a characteristic for which Cro-Magnon is well known) or potable art such as carvings. Although the two species may have coexisted towards the end of Neanderthals existence, it is not clear whether they were existing in the same areas simultaneously.

Repair of Tissues

The body has an incredible ability to heal itself. Whether you cut yourself cooking dinner or break a bone playing football (Figure 4), your body will invoke repair processes involving cell division to fix the problem. Some animals can even regenerate entire limbs that have been removed.

Apoptosis

The cell can activate a cell suicide program called apoptosis. It is a complex process that is one of the body's natural defense mechanisms. This is not the same as the way a damaged cell dies through a sloppy process called necrosis. Apoptosis is a programmed cell death as a clean way for cells to delete themselves and recycle many of its valuable components. The cell gently releases its connections to neighboring cells, produces digestive proteins that break it down into small fragments, and disintegrates into bite-sized pieces that are consumed by other body cells. Following apoptosis, the cell disappears without a trace. If a gene that is involved in apoptosis is itself damaged, it removes one of the cells repair mechanisms, making cancer development more likely. Apoptosis is a major reason why chemotherapy and radiation therapy work. Radiation therapy and many chemotherapy agents cause profound DNA damage—enough to induce apoptosis.Unfortunately, these treatments do not discriminate between cancer cells and normal cells. Any cell that is dividing is a potential target. In fact, the apoptosis of normal cells produces most of the side effects of chemotherapy and radiation therapy, including nausea and hair loss. -programmed cell death as a clean way for cells to delete themselves and recycle many of its valuable components.

Cell Cycle

The cell cycle can be partitioned into several phases. In the most general sense, it consists of the mitotic phase (M), when segregation and cytokinesis take place, and interphase, a long period of growth. Interphase can be further broken down into three subphases: Gap1 (G1), Synthesis (S), and Gap2 (G2). The cell cycle is the process by which cells divide. It can be divided in many ways, but is commonly broken down into interphase and mitosis, each of which can be subdivided further. -also known as cell-division cycle is the series of events that take place in a cell leading to its division and duplication (replication).

Anaphase I

The chromosomes are pulled apart from each other. Sister chromatids are kept together, while homologous chromosomes move to opposite poles. This is different from mitosis, where sister chromatids are separated.

Circulatory System

The circulatory system includes the heart, blood vessels and blood cells, and is derived entirely from mesoderm. The workhorse of the circulatory system, the heart, is the first fully functional organ in the embryo. Just 21 days after fertilization, two tubes fuse together forming a single-chambered heart capable of beating. It takes a few more weeks to fully form the four-chambered heart. Blood vessels do not sprout out from the heart, but originate elsewhere in the embryo. They grow longer, eventually connecting to the heart. Once the first circulatory loop is completed, the heart can pump blood through the embryo. The circulatory system is the lifeline of the embryo and performs functions not normally carried out by an adult circulatory system. For example, the embryo must obtain nourishment and oxygen before the intestine and lungs develop, and must get rid of waste before kidneys form. The embryonic circulatory system performs all these functions by connecting the embryo to the mother's circulatory system via the placenta.

Digestive System

The digestive system derives from endoderm and arises from the primitive gut, a long tube that forms around the same time as the single-chambered heart (Figure 11). The most anterior region of the gut forms the pharynx, which is shared between the digestive and respiratory systems. Moving from anterior to posterior, the foregut differentiates into the esophagus, stomach and intestines. This is how the digestive system differentiates - mesoderm surrounding the esophagus is different than mesoderm surrounding the stomach. Signals sent out from the different regions of mesoderm instruct the gut to become different structures along the length of the tube. Accessory organs, including the liver, gallbladder and pancreas, form by budding off from the main gut tube.

Stop Codon

The end of a gene is indicated by one of three codons, which do not translate into an amino acid and instead function as stop signals. These stop codons are TAG, TAA, and TGA (ATC, ATT, and ACT in the noncoding strand). Nucleotide codon that signals the end of an open reading frame and causes the termination of transcription because there is no tRNA with the corresponding anti-codon

Phenotype

The expression, or production of proteins from DNA, of the alleles within our DNA determines our outward appearance. This can be determined by the output of one gene or that of multiple genes. This is described as an individual's phenotype, or the observable traits of an organism. -the observable traits of an organism.

Fertilization

The first step of embryonic development is fertilization which is the fusion of a haploid (1N) sperm and a haploid (1N) egg to create a diploid (2N) zygote Sperm - lean, mean, fertilizing machines Egg - fertile grounds Fertilization releases the egg from its suspended state, triggering production of new proteins and initiation of the cell cycle (mitosis). Fusion event between egg and sperm that creates a new embryo.

Antigenic Drift (Flu Vaccine)

The flu vaccine that you get each year has three flu strains, two A strains and one B strain. The strains change from year to year because the influenza virus genes are made of RNA and can mutate much faster than genes made with DNA. Once you receive the vaccination, your body produces infection-fighting antibodies against the three flu strains in the vaccine. If you are around others who have the flu, the antibodies will latch onto the virus's Hemagglutinin (HA) antigens that help them to attach to healthy cells. So the virus can no longer infect you. But if a mutation in the viral RNA allows it to change and therefore change the shape of the HA antigens they will no longer be blocked from the antibodies in the vaccine that you got. Because antigens and antibodies have a key and lock mechanism that has to match each other to form a bond. This will allow the newly mutated virus to infect your body's cells. That is why every year we have to get the flu vaccine that has the most common and recent antibodies.

Double Helix

The formation of double stranded DNA by these rules creates a larger DNA structure known as the double helix. The two strands intertwine like a twisted ladder with the 5' to 3' interactions of the nucleotides on the outside like the rails of a ladder and the base pairing between the nitrogenous bases occurring on the inside forming "rungs".

Genetic Code

The nucleotide sequence in DNA is the "molecular alphabet" that encodes the amino acid sequence of proteins. This is also known as the genetic code. A triplet nucleotide code would provide at least 64 different amino acids (43) - more than enough possibilities for the 20 amino acids, and thus scientists discovered the triple nucleotide code known as a codon. Sets of three nucleotides that specify amino acids or stop codons during the process of translation at the ribosome; the set of rules by which information encoded in genetic material (DNA or RNA sequences) is translated into proteins (amino acid sequences).

Toumai

The oldest hominid fossil ever found was an almost complete skull nicknamed Toumai, discovered in Chad, Central Africa (species Sahelanthropus tchadensis) Toumai proved to have a small brain size (about 350 cubic centimeters - cc), and its spinal cord and skull connected at a posterior region (rather than central), features that are typical of apes. However, its brow ridges and small canine teeth place it closer to later hominids. These characteristics and its age (6-7 million years old) suggest it is the closest link to the common ancestor of humans and chimpanzees, but its exact position in the tree of man is still uncertain.

Open Reading Frame

The part of the genome that is "read" to make proteins is called an open reading frame. The open reading frame contains all of the codons to make a protein . A sequence of nucleotide codons (from start to stop) that encodes one protein

Transcription

The process by which mRNA is made from DNA is called transcription. In linguistics, transcription means conversion of a written source into another medium. In biology it means converting information from a DNA source into RNA. Both DNA and RNA use the nucleotide language, and the information is simply transcribed, or copied, from one molecule to the other. There are three major differences between an mRNA and DNA: 1) The 5 carbon sugar used to make up a mRNA nucleotide is ribose (RNA) instead of deoxyribose (DNA) 2) While DNA is composed of A, G, C, and T nucleotides, RNA uses A, G, C and U. The U stands for Uracil. Wherever you would see a "T" in DNA it would be a "U" in an RNA molecule (see Figure 5 of mRNA). 3) While DNA is primarily found in the double stranded form, mRNA is single stranded. The process of creating an mRNA from DNA using the protein enzyme RNA polymerase

DNA Replication

The process by which new copies of DNA are made. The basic steps include unwinding of double stranded DNA by helicase to make a template strand and synthesis of a new strand through addition of nucleotides by DNA polymerase The process of making new DNA strands is called DNA replication. During DNA replication every chromosome in a cell is copied by taking advantage of base pairing between single strands of DNA. Generally speaking, a copy of DNA is made by unwinding the double helix to create a single stranded template that is copied using base pairing. The first step of unwinding the double strand is done by a protein called helicase. The two single strands can now act as a template for making the opposite strand and a copy of DNA. Once the template for replication is made through unwinding the double helix, DNA is replicated using base pairing.

RNA Polymerase

The process of transcribing mRNA from DNA is performed by a protein called RNA polymerase. Remember transcription happens in the nucleus because that is where DNA that is being transcribed is located. The protein enzyme that creates an mRNA from the template strand of DNA

Spine

we are by no means perfectly adapted to bipedal locomotion. Our spines are a heritage from distant ancestors who carried themselves horizontally. As in modern quadrupeds, the spine functioned more like a flexible suspension bridge, supporting the body's organs. The human spine has been transformed from this, into a weight bearing column, putting it under unprecedented stress and dooming us to the likelihood of back injuries and pain.

Hemoglobin

The protein inside red blood cells that carries oxygen throughout the body

Helicase

The protein that unwinds double stranded DNA during DNA replication

Reproductive Cloning

The purpose of reproductive cloning is to create a new organism that is genetically identical to an existing one. In 1997, Scottish researchers reported the first successful cloning of a mammal - a sheep named Dolly. Reproductive cloning uses a technique called somatic cell nuclear transfer(SCNT), where the nucleus from a donor cell to be cloned is transferred into a recipient egg whose nucleus has been removed. The egg is tricked into thinking it is fertilized and the embryo is implanted into the uterus of a surrogate mother. Since the embryo has the exact same DNA as the donor cell, the embryo will be a genetic clone of the adult. Reproductive cloning has been reported for sheep, cows, mice, dogs, monkeys, and many other animals, and could be beneficial for the agricultural and pharmaceutical industry. Private speculators have even tried to cash in - one company (now out of business) offered to clone your favorite pet cat for $50,000! While a few rogue scientists claim they are trying to clone humans, nearly all scientists have no desire to clone human beings for reproductive purposes. It is illegal in many countries, including the United States, because of the ethical issues it raises. Cloning approach used to create an organism genetically identical to another

Polyspermy

The single sperm that fertilized the egg is probably not the only sperm in the vicinity. Fertilization by multiple sperm, called polyspermy, always results in embryonic death. Luckily, the zygote reacts quickly to prevent polyspermic fertilization by releasing enzymes to modify the protein "lock" on the zona pellucida so additional sperm are no longer able to bind. No binding means no fertilization. Disaster averted. The prevention of polyspermy is a negative feedback loop. Fertilization by multiple sperm; lethal for the embryo.

Anaphase II

The sister chromatids are pulled to opposite poles of the cell.

Sperm

The sperm's role in fertilization is fairly simple, they travel through the female reproductive tract, find the egg and deposit chromosomes. Sperm are much smaller than female eggs (see Figure 2) and there is a very good reason for this. Human males release over 250 million sperm during each ejaculation. Since so many sperm are continually produced, the male body cannot afford to invest a lot of energy or resources in something that is quickly discarded. So each sperm cell is designed to be a compact and efficient package that contains only the resources it needs to get the job done: (1) A haploid (1N) nucleus containing the father's chromosomes. (2) A tail that propels the sperm on its journey to the egg. (3) Mitochondria that generate energy (ATP) to power the tail. (4) A sac, called the acrosome, containing enzymes that allow the sperm to enter the egg.

Inheritance

The variation in some traits is heritable or is consistently passed on from parent to offspring. Other traits are strongly influenced by environmental conditions and show weak heritability.

Environmental Chemicals

The widespread use of agricultural pesticides can also cause developmental defects. For example, in the 1950s and 1960s, methylmercury was used to kill fungus in wheat and grain fields. Mothers who ate bread or drank water contaminated with methylmercury gave birth to children with decreased mental functioning. Some animals are more sensitive to teratogenic agents than humans, and can serve as "biosensors" telling us when harmful chemicals are present. For example, 5 miles from my hometown in Minnesota, a group of school kids exploring a pond found that 40% of the frogs had missing or extra limbs. Scientists descended upon the town to identify the cause of the deformities. No definitive cause has been found yet, but some research suggests that a pesticide used by local farmers can cause limb deformities in laboratory frogs by either interfering with the retinoic acid pathway or enhancing the ability of parasites to infect the frogs. It has not been determined whether the teratogenic agent has affected humans in the area, but a local resident noticed that at least one person in every household surrounding the wetland has cancer.

Blood Types

There are four basic blood types, and they are O, A, B, and AB. We know that our blood type is determined by the alleles that we inherit from our parents. For the blood type gene, there are three basic blood type alleles: A, B, and O. We all have two alleles, one inherited from each parent. The possible combinations of the three alleles are OO, AO, BO, AA, BB and AB. Blood types A and B are "co-dominant" alleles, whereas O is "recessive". Like a dominant allele, the presence of a single co-dominant allele is sufficient to influence the phenotype; a recessive phenotype is apparent only if two recessive alleles are present. Because blood type O is recessive, it is not apparent if the person inherits an A or B allele along with it. So, the possible allele combinations result in a particular blood type in this way: OO = blood type O (recessive) AO = blood type A (A is dominant, masking O) BO = blood type B (B is dominant, masking O) AA = blood type A BB = blood type B AB = blood type AB (co-dominant, both alleles involved in phenotype) You can see that a person with blood type B may have a B and an O allele, or they may have two B alleles. If both parents are blood type B and both have a B and a recessive O, then their children will either be BB, BO, or OO. If the child is BB or BO, they have blood type B. If the child is OO, he or she will have blood type O.

Cell Cycle Checkpoints

There are four phases of the cell cycle that are tightly regulated by CELL CYCLE CHECKPOINTS and certain CELL CYCLE PROTEINS. The proteins are the sensors and signal to the cell cycle checkpoints (the comparator) that the cell cycle can progress to the next phase. Once the checkpoints get the go ahead from the cell cycle proteins to proceed to the phase where DNA is replicated, DNA replication takes place to make 2 DNA molecules through the processes we just learned about. Once the cell cycle has committed to making DNA, the cell continues through the cycle to divide and the process starts over again. When the cell cycle proteins signal that the cell is ready to proceed through the cell cycle, the loop is turned ON and DNA replication moves forward. If the cell cycle proteins do not signal to proceed, the loop is OFF and DNA replication does not occur.

Exceptions to Mendel's Principles

There are many examples of inheritance that appear to be exceptions to Mendel's laws. Usually, they turn out to represent complex interactions among various allelic conditions. For example, co-dominant alleles both contribute to a phenotype. Neither is dominant over the other. Control of the human blood group system provides a good example of co-dominant alleles.

Cyclin-Dependent Kinases (CDKs)

There are several types of CDK that are responsible for progression through different stages of the cell cycle. Kinases are a family of proteins that add phosphate groups to other molecules through a process known as phosphorylation. However, CDKs do not phosphorylate target proteins unless they themselves are activated. CDKs are activated after being bound to proteins known as cyclins. Once cyclin-CDK complexes are formed, the CDK is activated and able to phopshorylate its target protein. CDKs have multiple targets that they interact with at different steps of the cell cycle, each of which may require different cyclin/CDK combinations. CDKs are always present at about the same level within a cell, but this does not lead to aberrant cell cycling because they inactive unless bound to the appropriate cyclins. The amount of cyclin molecules present, and which cyclins are present, varies throughout the cell cycle in response to a variety of factors. For instance, a molecular cue exists to alert the cell that microtubules have attached to the kinetochores, making it okay to proceed to anaphase. This is an example of an internal signal that comes from within the cell. External signals also exist, such as the presence of growth factors. Each of the cyclin-CDK complexes functions to sense whether or not the required conditions have been met before sending a signal for the cell cycle to continue.

Molecular Evidence of Common Ancestor

There is a reason Hox genes are so important for many of the developmental processes we have discussed - they make up an ancient gene family present in all animal species. They also carry out the same function which is to pattern the body plan of the early embryo. Hox genes required for anterior structures in the fruit fly are also required for anterior structures in the human; the same holds true for Hox genes required for posterior structures. Hox genes lie right next to each other on the chromosome in a cluster, with genes at the 3' end being required for anterior patterning, and genes at the 5' end for posterior patterning. It is highly unlikely that Hox gene sequence, chromosomal arrangement, and function would be so highly conserved unless all animals shared a common ancestor. Hox genes therefore provide excellent support for the theory of evolution. During evolution the Hox gene clusters duplicated. For example, fruit flies have one copy of the cluster, while humans have four copies (Figure 14). The duplication of Hox genes might help explain why an ancestral body plan could diverge along separate paths, with one path leading to the fruit fly and another to humans. Early anterior-posterior patterning in the embryo requires Hox genes, which is why they are conserved. However, in humans there are four copies. One copy would stay unchanged to perform the conserved function, leaving the other three copies free to experiment with new roles, such as forming vertebrae, a structure not present in flies.

Insertion/Deletion

These mutations are as they sound - an extra nucleotide or multiple nucleotides are inserted into a DNA sequence, or one or many nucleotides are missing from a nucleotide sequence. Deletion: A type of DNA mutation that occurs when one or more nucleotides is removed from the nucleotide sequence. These mutations often result in frameshift. Insertion: A type of DNA mutation that inserts extra nucleotides in a nucleotide sequence; insertions often lead to frameshits

The First Family & Adar Skull

They had broad heels that could withstand the upright gait and spongy shock absorbing bones rather than the more solid bones in the heels of apes. Although their toe bones are longer compared to modern humans they do not curve towards the heel as they do in modern tree climbing apes.

Galapagos Finches and Inheritance

They marked every bird using bird rings of different colors and and they found the nests of the birds and marked the hatchlings so that they knew the parents of the baby birds. When they looked at the bill size of the parents and the bill size of the adult baby birds they found that if the parent birds have big bills the baby birds are going to have big bills. Heritability--> variation is heritable

Anti-parallel Single Strands

This means the two strands are side by side in opposite directions. One runs from the 5' carbon to 3' carbon while the second lays in the opposite 3' to 5' direction.

DNA Polymerase

This process of creating a new strand from a template strand of DNA is performed by a protein known as a DNA polymerase. The name of this protein comes from the fact that the function of a DNA polymerase is to take individual nucleotides and put them together to make a new polymer (or strand) of DNA. The protein responsible for synthesizing new DNA strands through base pairing

Meiosis I

This process separates homologous chromosomes into two haploid daughter cells. Interphase 1, Prophase 1, Metaphase 1, Anaphase 1, Telophase 1

Meiosis II

This process serves to separate sister chromatids, ultimately generating 4 haploid cells from the original cell. Prophase II, Metaphase II, Anaphase II, Telophase II

Substitution

This type of mutation occurs when one nucleotide is replaced by another (Figure 1). Sometimes substitutions do not affect the amino acid sequence because multiple codons can encode for a given amino acid. These are called silent mutations. In other cases, the substituted nucleotide can change the codon to encode for a different amino acid that can affect the resulting protein. Substitutions can also change the codon to a STOP codon causing the production of a truncated and likely nonfunctional protein.

Germ Layers

Three layers of the embryo established during gastrulation; ectoderm (outer), mesoderm (middle), and endoderm (inner) cell layers.

Cell Checkpoints

To ensure that these events proceed in the proper order, a series of checkpoints exist in the cell cycle. These checkpoints provided the necessary signals for the cell cycle to proceed. There are multiple checkpoints spread throughout the cell cycle (Figure 13). These transitions are governed by a family of enzymes known as cyclin-dependent kinases (CDKs).

Initiation

Transcription begins with RNA polymerase binding to the promoter. RNA polymerase unwinds double stranded DNA and starts RNA synthesis.

Differentiation

Transformation of a cell into a more specialized role through the acquisition of genetic changes and physical characteristics; for example from a stem cell into a blood cell or neuron. This incredible transformation where cells acquire characteristic changes in size, shape, and function in order to perform a special role in body maintenance is called differentiation.

Trisomy 16

Trisomy 16 (3 copies of chromosome 16) is the most common disjunction event in humans, occuring in 1% of all pregnancies. As one of the body's many feedback mechanisms, this is normally detected and miscarriage is induced during the first trimester.

Vector

Typically for gene therapies to be performed a carrier or vector must be used to introduce the normal gene into a patient's cells. The most common vector used in gene therapy are disabled viruses. The vector can be injected directly into a specific tissue in the body or given intravenously (by IV), where it is taken up by individual cells. Alternatively, a sample of the patient's cells can be removed and exposed to the vector in a laboratory setting. The cells containing the vector are then returned to the patient. Once the new gene is introduced to the cell in this manner, it can produce the normal protein to counteract the problems created by the abnormal protein.

Pluripotent Stem Cells

Undifferentiated cells that have the ability to form every cell type that will be present in the future embryo. can give rise to most, but not all, cell types. A perfect example is the inner cell mass of the blastocyst. These cells can form all cell types of the future embryo, but cannot contribute to the placenta (which is the job of the outer trophoblast cell layer). Human pluripotent cells are commonly referred to as embryonic stem cells since they can form ectoderm, mesoderm, endoderm, and all the cell types derived from these germ layers.

Availability of Variation

Variation is reflected at both the organism's genotype and phenotype levels. It is at the level of genetic variation that selective forces act upon to bring change in gene frequency within a population over time. The key is that genotype is heritable and passed on to the next generation. Yet, since an individual's genotype often influences its phenotype, the phenotypes within a population are also subjected to change.

Semi Conservative Replication

When DNA replication is complete one double stranded piece of DNA will have been separated and from each single strand the opposite strand will have been made. The result is two new double helicies each containing one strand from the original molecule and one newly synthesized strand. This pairing between old and new strands is known as semi-conservative replication. The term to describe the nature of DNA replication. Two new DNA molecules are made from one original molecule. Each new DNA molecule has one strand from the original molecule and a new strand.

Body Axes

While gastrulation determines which cells will form internal vs. external structures, the body plan must be further refined by setting up three body axes: the anterior-posterior, dorsal-ventral and left-right axes

Epigenetic Gene Silencing

While many heritable disorders in humans are caused by DNA sequence changes (mutations) that abolish gene expression or alter protein function, a number of human diseases are caused by inappropriate gene silencing brought about by epigenetic modifications. Indeed, most cancers involve the epigenetic silencing of genes that normally regulate cell proliferation. The major forms of epigenetic gene silencing occurring in human tumors are DNA methylation and histone deacetylation.

Therapeutic Cloning

While the goal of reproductive cloning is to recreate an entire organism, therapeutic cloning generates stem cells to be used in the laboratory to study cell differentiation and to develop treatments for diseases. It stops well short of creating a whole new organism. There are a number of methods used to create therapeutic stem cells, which we will discuss below. The field of stem cell research is still fairly new and has a long way to go before cures for human disease can be found, but much progress has already been made. While some religious and political groups oppose therapeutic cloning because it can involve destruction of a blastocyst-stage embryo, most of the general public and scientists support it because of the therapeutic potential. Cloning approach that generates stem cells for use for medical and research purposes

Egg

While the sperm is a lean, mean, motile machine, the female egg provides a rich, nurturing environment that supports the embryo until it starts producing proteins on its own and is able to obtain nutrients from the mother. The egg contains a haploid (1N) nucleus and a huge volume of cytoplasm where many of the proteins and mRNAs the embryo needs to survive early development are stored. Two protective barriers surround the egg to regulate sperm entry are the cumulus cells and the zona pellucida. Unlike sperm, which are continuously produced, all the eggs a female will ever need are present in ovaries at birth. Eggs remain inactive until triggered by menstrual hormones and one egg is released during each menstrual cycle. The menstrual cycle will be discussed in more detail in upcoming modules. Following intercourse, sperm deposited in the female's reproductive tract start swimming upstream with their motile tails (similar to salmon swimming upstream to spawn) using ATP as an energy source. If the timing is right, the sperm will encounter a freshly ovulated egg in the fallopian tube (also called the oviduct). Good timing is essential since the sperm need to be in the female reproductive tract long enough to become activated, or capacitated, but not so long that they die. Sperm are usually capable of fertilizing an egg anywhere from several hours to 5 days after intercourse. In contrast to long-lived sperm, the egg has only 24 hours to encounter a sperm before it dies.

Cell Communication

While transcription factors regulate what is happening inside a cell, additional information on how a cell should differentiate is also provided from the outside environment. Any given cell in an embryo is not isolated, but rather is surrounded by many other cells that are in constant communication. Signals are sent between cells so they can instruct each other. These signals can be bound to a cell's surface, or floating around in the extracellular space. You will discuss cell communication in more detail later in the semester, but for now, just understand that communication and interaction between neighboring cells can provide cues for cells to differentiate. Signals from the outside of a cell are converted into information inside the cell. As with transcription factors, this information leads to tissue-specific gene expression, which produces proteins required for differentiation.

Are we genetically different from our Homo sapien ancestors who lived 10-20,000 years ago?

Yes. It is very likely that the rate of evolution for our species has continuously accelerated since the end of the last ice age, roughly 10,000 years ago. This is mostly due to the fact that our human population has explosively grown and moved into new kinds of environments, including cities, where we have been subject to new natural selection pressures.

Trisomy 21

You are likely more familiar with trisomy 21, or Down's syndrome (Figure 20). Down's syndrome, and other trisomy of autosomes (non-sex chromosomes) is associated with birth defects, mental retardation, and reduced life expectancy.

Codon

a "word" in DNA and RNA language that a protein can understand. One codon encodes for one amino acid. Because there are 64 possible codons, this also means that one amino acid can have more than one three letter code. "Words" of the DNA/RNA language, sets of three nucleotides that code for a particular amino acid

Population

a collection of interbreeding organisms of a particular species

Analogous

a dolphin is more closely related to a human than it is to a shark because dolphins are mammals. Similarly, bats and birds can both fly but their forelimbs are not homologous because they do not share a common ancestor that gave rise to the forelimb. The bat's wing was independently derived from the bird's wing. They are analogous structures. Convergent Evolution -structures that look similar but were not present in the last common ancestor. These structures have different ancestors but similar functions.

Tree Savanna Stage

a full transition from the Rain Forest Stage characteristic of chimpanzees.

Hox

a gene that controls the development of body plans in all animals.

Sexually Reproducing Species

a group of individuals that interbreed in nature

Adaptation

a process in which over many generations, a population becomes more suited to its habitat. Adaptation also refers to the trait that provides enhanced fitness, and therefore, is a product of natural selection. Favorable characteristics for a new environment from the original population can result in the population genetically adapting to the new environment. Such genetic changes can result in adaptations that occur at the structural, physiological, behavioral, cellular or molecular level over many generations and long time periods. However, if the habitat or environmental change is rapid, species may be less adapted to the environment and may become extinct over time. The criteria to define a trait as an adaptation must include factors like heritability and functionality at the present moment -the process in which over many generations, a population becomes more suited to its habitat. i.e. habitat tracking

Brain Size

a second major adaptive advantage that appeared later in human evolution was bigger brains. Brain size can be predicted by the skull-size of fossils of hominids. However, brain size gives only limited information about the internal structure and capabilities of the brain. As brain size increased, new capabilities evolved as well, such as using fire, giving these early humans abilities to adapt to and modify their environments. Tools became more sophisticated and eventually humans developed culturally as well as biologically. -Early hominids such as the Australopithecines had brains the size of modern apes (400 to 500 cm3) -Homo habilis with a brain of about 650 cm3, was probably the first hominid discovered to make and use stone tools -Another earlier hominid, Homo erectus, with a brain size ranging from 1200 to 1600 cm3 was the first to develop human-like culture. Homo erectus used tools, such as hand axes, made fires, and were the first hominid species believed to have spread from Africa into Asia. -Modern humans, Homo sapiens sapiens (brains ranging from 1200 to 1600 cm3), have even more sophisticated capabilities, probably due to neurological developments within the brain rather than size alone. -One later hominid species, Homo neanderthalensis, had a brain size of over 1300 cm3 but is considered to have been much less sophisticated than, and possibly even driven to extinction by, modern humans.

Molecular Evidence

a simple, repeated pattern underlay the differing body structures of animals. It could be seen in the segmented bodies of worms, in the vertebrae of animals with backbones, and in the head-thorax-abdomen construction of insects. In all of these, modular units like Lego blocks were arranged in a front-to-back line down the center of the body. The development of body plans in all animals is controlled by a remarkably small number of genes called the Hox genes and are virtually identical in all animals. The DNA code in Hox genes directs the cell to make chemical sequences, which regulate other genes that affect the positioning of cells in the embryo. Hox genes explained the discontinuous jumps in body form found in the evolution of species because a mutation in one gene could result in large changes in the organism from one generation to the next.

Anti-Codon

a three base region within a tRNA which specifically complements a particular nucleotide codon. three letter code on tRNAs that complement three letter codon on mRNAs

Vestigial Structure

a trait that was an adaptation for an organism's ancestor but it is no longer functional, cannot be considered an adaptation. For instance, the coccyx (a tail bone) is a vestigial tail in humans with no apparent structural or physiological function. Humans have over 100 vestigial structures

Kinases

a type of enzyme that transfers phosphate groups from high-energy donor molecules, such as ATP, to specific target molecules (substrates); the process is termed phosphorylation (the addition of a phosphate group to a protein or other organic molecule).

Population Phenotype

all its observable characteristics

Histones

are the chief protein components of chromatin. They act as spools around which DNA winds and they play a role in gene regulation, and without histones, the unwound DNA in chromosomes would be very long.

Terminally Differentiated Cells

are the end product of differentiation. They have acquired all the characteristics necessary to perform a specific function and are not capable of self-renewal. Neurons, cardiac muscle cells, and red blood cells are examples of terminally differentiated cells. Differentiated cells with the same characteristics group together to form tissues.

Jean Baptist-Lamarck

argued that species change over time into new species. Historians prefer the contemporary word 'transformism' to describe Lamarck's idea. Lamark proposed two mechanisms that could explain how organismal change or evolution takes place. He argued that species' lineages persisted indefinitely, changing from one form into another. Lamarck explained that species changed because of 'internal forces' that he described as some sort of an unknown mechanism within an organism causing it to produce offspring slightly different from itself. The changes accumulated over many generations became visible transformations and if enough changes took place, this transformation would result in new species. This was the first mechanism that he put forth to explain how species changed or evolved. The second is the one we today remember him for. He said that as an organism develops, it acquires many individual biological characters because of the organisms history of diseases, the way in which the organism uses its body and also due to accidents. He further argued that species can then become transformed if these individually acquired modifications were inherited by the individual's offspring, and further modifications were added through time. This is called the inheritance of acquired characteristics. Lamarck argued that ancestral giraffes had stretched to reach leaves higher up trees that caused caused their necks to grow slightly longer. These longer necks were inherited by their offspring who then were more likely to grow even longer necks than their parents. Using the giraffe's neck, he explained that after many generations of neck-stretching the giraffes became long necked as we find them today.

Nitrogenous Base

attached to the 1' carbon of the sugar. There are four different types of nitrogenous bases that can bind a deoxyribose sugar to make a nucleotide. These four bases fall into two groups: Pyrimidines & Purines. group attached to the 1' carbon of DNA and RNA. There are 4 bases in DNA, adenine (A), cytosine (C), guanine (G), and thymine (T)

"On the Origin of Species by Means of Natural Selection, or the Preservation of Favored Races in the Struggle for Life"

by Darwin, 1859 and presented a mechanism for evolution. He proposed the mechanism, natural selection, by which evolution occurs.

Dogma

dogma" is simply an established opinion among a group of people. The "central dogma of molecular biology" is an established opinion held among molecular biologists pertaining to the flow of cellular information from the three main macromolecules of molecular biology, DNA, RNA, and proteins. These molecules are different forms of the same information required to run the cell. The central dogma says that the flow of cellular information (the information required for a cell to live) flows from: DNA --> RNA --> Protein It also states this process is unidirectional meaning it NEVER flows from protein to RNA or RNA to DNA.

Antagonistic Coevolution

ex: Old World Swallowtail (Papilio machaon) caterpillar which lives on a plant called Fringed Rue (Ruta chalepensis). Rue plant produces etheric oils which repel plant-eating insects, but the caterpillar has developed resistance to these poisonous substances, thus reducing competition of other plant-eating insects

Fossils and Evolution

ex: The fossil record contains evidence for simple to complex forms of evolution of the eye

Cro-Magnon Man

first fossils of early modern humans, Homo sapiens, to be identified were found in 1868 in a 23,000-27,000 year old Cro-Magnon rock shelter in the Dordogne Valley rock site near the village of Les Eyzies in southwestern France. They were subsequently named the Cro-Magnon people. They were very similar in appearance to modern Europeans. Males were 5 feet 4 inches to 6 feet tall (1.6-1.8 m.) That was 4-12 inches (10-31 cm.) taller than Neanderthals. Their skeletons and musculature generally were less massive than the Neanderthals. The Cro-Magnon had broad, small faces with pointed chins and high foreheads.

Nucleosomes

form the fundamental repeating units of eukaryotic chromatin, which is used to pack the large eukaryotic genomes into the nucleus while still ensuring appropriate access to it (in mammalian cells approximately 2 m of linear DNA have to be packed into a nucleus of roughly 10 µm diameter). They are folded through a series of successively higher order structures to eventually form a chromosome; this both compacts DNA and creates an added layer of regulatory control which ensures correct gene expression.

How is Protein Made from mRNA?

genetic information is stored inside the nucleus as DNA, but proteins are made in the cytoplasm. That is why DNA needs mRNA to act as a messenger to carry the genetic information from the nucleus where DNA is located to the cytoplasm where it can be used to make proteins. After transcription has been completed in the nucleus, mRNA is transported to the cytoplasm. Once in the cytoplasm, mRNA is ready to convert the DNA language into protein language (amino acids) through a process called translation.

The Founders Effect

happens when a small fraction of a population splits off and goes to become a pioneer of a new population at a different location (Fig. 25). A small population will have a greater founder effect because the allele distribution in the new population may not be representative of the original one. Overall, genetic drift will decrease the genetic variation of the original population.

Coevolution in Hummingbirds and Ornithophilous (Bird-loving) Flowers

have evolved special biological characteristics that support each other or form a mutualistic relationship. Hummingbird flowers have nectar chemistry that support the bird's diet and the flower's color, shape, and size characteristics also coincide with the bird's vision and morphology. Flowers bloom during the hummingbirds' breeding seasons.

Totipotent Stem Cells

have unlimited potential and can form every type of cell. In humans, totipotent cells are present from the point of fertilization (the zygote) through the first several cleavage divisions. These cells can form any cell type in the future embryo, as well as the extra-embryonic tissues like the placenta.

Bipedalism (the Ancient Walk)

in A. afarensis came with one of the most significant discoveries in human evolution, the footprints of what now is thought to be two A. afarensis walking side-by-side in Laetoli, Tanzania. The computer simulation from the gait of these hominids from the 3.6 million years ago footprints (the ancient walk,) suggests that indeed Lucy walked upright similarly to modern men "It stands as perhaps the salient point that differentiates the forebears of man from other primates. This unique ability freed the hands for myriad possibilities -- carrying, tool-making, intricate manipulations. From this single development, in fact, stems all modern technology"- Mary Leaky

Base Pairing

interaction between nitrogenous bases on nucleotides to form double stranded DNA it is the nitrogenous bases that are used to create a double stranded DNA molecule. Double stranded DNA contains two anti-parallel single strands. Base pairing always occurs between a purine and a pyrimidine. Adenine ALWAYS pairs with Thymine (A-T) Guanine ALWAYS pairs with Cytosine (G-C)

Chromatin

is the complex combination of DNA, RNA, and protein that makes up chromosomes; and it's found inside the nuclei of eukaryotic cells (organism whose cells contain complex structures enclosed within membranes), and within the nucleoid in prokaryotic cells. It is divided between heterochromatin (condensed) and euchromatin (extended) forms. The functions of chromatin are to package DNA into a smaller volume to fit in the cell, to strengthen the DNA to allow mitosis and meiosis, and to serve as a mechanism to control expression and DNA replication

Neo-Darwinism

it was not until the emergence of the modern evolutionary synthesis from the 1930s to the 1950s that a broad consensus developed that natural selection was the basic mechanism of evolution that led to neo-Darwinism or the synthetic theory of evolution. The synthesis of the two ideas, Darwin's theory of evolution and Mendelian genetics, is called Neo-Darwinism or the synthetic theory of evolution. During the 1930s and 1940s, Neo-Darwinism gradually spread through all areas of biology and became widely accepted. It unified genetics, systematics, paleontology, classical comparative morphology, and embryology. -the synthesis of Darwin's theory of evolution and Mendelian genetics, also known as the synthetic theory of evolution.

Hominids

members of the family of humans or human like species. The hominid branch has a history of about 8 million years, the time when the earliest ancestors of humans diverged from the apes. This branch has at least a dozen hominids that have lived on earth. Although there are about fifteen species categorized, this categorization is not definite because fossils are not easy to neatly separate into species. In addition, like all creatures while no two hominids were alike, it is not clear when a new species began and ended. Further, this list is incomplete because as scientists find new fossil hominids, the hominid family tree grows new branches. There is, however, one thing that is clear: over the millions of years species existed hominids changed and evolved and adapted to new environmental conditions. Some species diverged or separated into new species.

mRNA

messenger RNA In the nucleus, mRNA decodes the DNA words that make one protein and then takes this message to the cytoplasm where it is translated into an amino acid sequence, the primary protein structure. mRNA is made as a copy, or "transcript," of the DNA in the nucleus through transcription, and that transcript is translated into a protein in the cytoplasm A molecule of RNA encoding the information for a protein product. mRNA is transcribed from a DNA template, and carries coding information from the nucleus to the sites of protein synthesis in the cytoplasm, the ribosomes -(5' -> 3') (mRNA made from Template strand)

Galapagos Finches and Population Growth

n every generation there are more offspring produced than that can survive. They also showed that the abundance of finches were closely correlated with the abundance of resources which is, in this case, seeds that the birds eat.

Pyrimidines

nitrogenous bases with one carbon ring Cytosine - C, Thymine - T

Purines

nitrogenous bases with two carbon rings Adenine - A, Guanine - G

The Bottleneck Effect

occurs when a significant portion of a population is removed by some random event such as natural disaster (e.g. earthquake), disease (e. g. yellow fever) or selective predation. This would be a dramatic effect if this loss of alleles happens in a small population compared to a big one.

Environment's Affect on Bipedalism

one of the favorite explanations for the transition to bipedality has centered on drastic environmental changes that swept Africa more than five million years ago. By that time, the global climate had become significantly cooler and drier. This resulted in advancing grasslands in sub-Sahara Africa while the rain forests contracted, shrinking the habitat where tree-dwelling primates lived and foraged.

Directional Selection

one side or the other of your bell curve is selected for.

Variation

organisms within populations exhibit individual variation in appearance and behavior. We see differences in body size, hair color, facial markings, voice properties, or number of offspring. However, some traits show little to no variation among individuals (ie. number of eyes) Variation between individuals in traits is displayed in all life forms at the genetic level. A prerequisite for evolution through natural selection is the availability of variation in traits within individuals in a population. Variation is reflected in both the organism's genotype (the set of genes that it carries) and phenotype (all its observable characteristics). It is at the level of genetic variation that selective forces act upon to bring change in gene frequency within a population (a collection of inter-breeding organisms of a particular species) over time. The key is that genotype is heritable and passed on to the next generation. Yet, since an individual's genotype often influences its phenotype, the phenotypes within a population are also subjected to change.

Fossil

preserved remains of an organism from a remote past.

3 Mechanisms of Variation

promote evolution 1. Mutations that occurs in the organism's DNA 2. Gene flow 3. Genetic drift that occurs at the population level.

Gamete

reproductive cells Reproductive cell, such as an egg or sperm, formed during meiosis; carries a haploid (1N) set of chromosomes -is a cell that fuses with another gamete during fertilization (conception) in organisms that reproduce sexually. A female is any individual that produces the larger type of gamete, called an ovum (egg) and a male produces the smaller tadpole-like type, called a sperm.

Apes

shared perfect identity with 96% of our DNA sequence. This is irrefutable evidence that our relationship to apes goes beyond just simple resemblance. our lineages separated about 5 to 10 million years ago, when chimpanzees and hominids started evolving independently it is clear that despite the genetic similarity, we have not directly evolved from chimpanzees as most people and the media tend to think.

Bioremediation & Biodiversity Crisis

some grasses and other plants have become adapted to soils highly polluted with nickel and other toxic heavy metals. Extensive studies of the systematics, genetics, and physiology of these plants have laid the foundation for techniques for re-vegetating and stabilizing soils made barren by mining activities, and even for detoxifying metal-contaminated soil and water. It has been found that some bacteria have the capacity to metabolize mercury to a less toxic form, and their genes for this capacity have been transferred into plants in laboratory experiments. In other cases, plants that have evolved the capacity to "hyperaccumulate" heavy metals and thus withstand toxic soils, are currently being used commercially as a cleanup technology. As a result of human activity, genetically unique species and populations are becoming extinct at an alarming rate. Our activities threaten not only conspicuous species, such as large mammals (i.e. Mexican Wolf) and sea turtles, but also innumerable plants, arthropods, and other lesser-known organisms, which collectively are a potential source of natural products, pest control agents, and other useful services. They also recycle chemical elements that enables the entire ecosystem to operate. Evolutionary biology is playing a major role in addressing this "biodiversity crisis." An important consideration is which species, ecological communities, or geographic regions merit the most urgent conservation efforts, since there are economic, political, and informational limits on the number of species we can save.

Mutualistic Relationship

species have evolved special biological characteristics that support each other to form a relationship where they benefit each other.

Fitness

the ability of an organism to pass on survival-favoring attributes to their offspring Fitness is NOT a property of an organism. There is not such a thing as "only the strong survives". To be "fit" is not an issue of who is the strongest, fastest, or biggest. The fitness of an organism pretty much depends on its environment. For instance, if the Earth's temperature were to be reduced dramatically to the levels of the previous ice ages (the most recent one peaked around 11,000 years ago), it is highly probable that an organism's fittest traits today will cease to be favorable during extremely cold temperatures conditions. Also, the exuberant tail of the peacock is thought to be the result of sexual selection by females. The peacock in figure 28 is an albino; selection against albinos in nature is intense because they are easily spotted by predators or are unsuccessful in competition for mates. Peacocks with the multi colored tail are sexually selected or are preferred for mating. Therefore, we can conclude that fitness is shaped by the environment. Favorable traits are those ensuring an organism's survival and reproduction relative to the environment it is living in. It is important to understand that although natural selection acts on individuals, the effects of chance mean that fitness can only really be defined "on average" for the individuals within a population. When considering a particular genotype, its fitness corresponds to the average effect on all individuals with that genotype. As in the example of many human genetic disorders such as cystic fibrosis, very low-fitness genotypes cause their bearers to have few or no offspring on average.

Fossil Age

the age of any fossil can be measured if the geological stratum where it was found is known. Certain rocks, particularly lavas and other volcanic deposits, contain radioactive minerals which decay at a constant rate over time. For example, uranium has a half-life of 4.5 million years and produces lead in this long process. Therefore, a ratio between uranium and lead can determine the age of any given rock where a fossil is found. The totality of fossils with their placement in rock formations and sedimentary layers is called the fossil record. The fossil record is a direct testament of how the history of life unfolded on Earth. The minimum age to distinguish a fossil from an ordinary remain is set arbitrarily at 10,000 years from the present.

The Coding Strand

the coding strand of DNA during transcription that contains the nucleotide codons in the correct order to be read. However, the coding strand is NOT the one used to make mRNA. When mRNA is made using the non-coding DNA strand, the resulting mRNA strand will actually have the same sequence (except U instead of T) as the DNA coding strand. the single strand within a DNA double helix that contains the nucleotide codons in the correct order to be read. This DNA strand has the same sequence as the transcribed mRNA (given U in RNA and T in DNA). Runs 5'-3'

Human Genome Project

the completion of the human genome project represents one of the major advancements in human history (Fig. 26). Likewise, different genome projects have been completed for organisms such as the bacterium, yeast, nematode, fruit fly, newt, lungfish, and flowering plants. The analysis of similarities between DNA sequences from different organisms holds a tremendous potential to frame many evolutionary questions at the molecular level. Now we can begin to establish evolutionary relationships between organisms by comparing their cell organelles, development of their embryos with body plans, and the vertebrate immune systems, among other cellular and molecular aspects. It is predicted that various pending questions about similarities and differences between humans and our closest relatives will be addressed by data from the field of genomics.

Respiratory System

the digestive and respiratory systems are intimately connected. Normally the pharynx is open to the trachea so that you can breath freely. But when you swallow, a flap of tissue (called the epiglottis) folds down and covers the opening to the trachea, diverting the food into the esophagus. This prevents you from choking. It turns out that the respiratory and digestive systems have the same origin - the foregut tube! During development, the foregut tube projects outward just below the pharynx and forms a new tube that develops into the trachea (windpipe) and lungs (Figure 12). This new tube branches at the bottom to form the left and right sides of the lungs. The lungs are one of the last organs to fully form and differentiate, which explains why many premature babies have trouble breathing. In order for a baby to breathe on its own, the lungs must secrete a substance called surfactant, which is produced toward the end of pregnancy. Premature babies are often put on ventilators to help them breathe, and artificial surfactant can be delivered until the lungs are developed enough to produce surfactant on their own.

Left-Right Axes

the imaginary line between the two lateral sides of your body. Even though humans look symmetrical along this axis from the outside, inside we are asymmetric. Your heart is on the left side of your body, while your liver is on the right.

Anterior-Posterior Axes

the imaginary line extending from the top of your head to the tip of your toes. Anterior is toward the top, posterior toward the bottom.

Dorsal-Ventral Axes

the imaginary line extending from your back to your belly. The dorsal fin of fish, dolphins, and whales got its name because this fin is located on their backs. Your spinal cord is a dorsal structure, while your belly button is a ventral one.

Stasis

the lineages do not change much for a long time. Coelacanths is a good example of stasis. It is a fish lineage that branched off of the tree near the base of the vertebrate clade. Until 1938, scientists thought that coelacanths went extinct 80 million years ago. Then they discovered a living coelacanth from a population in the Indian Ocean that looked very similar to its fossil ancestors. Coelacanth lineage exhibits about 80 million years worth of morphological statis. Ginkgo biloba is an example of a living fossil tree that is similar to the fossils found from 170 million years ago.

Single Stranded DNA

the linking of 5' and 3' carbons between nucleotides to create one strand of DNA

Mitosis

the process by which somatic cells divide. mitosis refers to the portion of the cell cycle when chromosomes are separated from each other. However, the word mitosis is also commonly used to refer to the complete cell cycle in somatic cells. After interphase is complete, the mitotic phase can proceed. Mitosis(Greek "mitos" = thread) is the process bywhich a eukaryotic cell separates its chromosomes into two pairs. Like interphase, mitosis can be subdivided into several stages: Prophase, Prometaphase, Metaphase, Anaphase, Telophase

Host-Parasite Coevolution

the reciprocal adaptive genetic change of two antagonists (e.g. different species or genes) coevolve through reciprocal selective pressures. Diseases that you may be familiar with such as malaria, AIDS and common influenza are caused by coevolving parasites. -the reciprocal adaptive genetic change of two antagonists who have coevolved through reciprocal selective pressures.

Population Genotype

the set of genes that it carries

Paleoanthropology

the study of human origins and evolution from our ape-like ancestors. Studying our origin from the deep past, over millions of years, allows us to understand the universal and defining traits that make our species what it is.

Biogeography

the study of the distribution of life forms over geographical areas. Biogeography not only provides significant inferential evidence for evolution and common descent, but it also provides testable predictions. Biogeography is split into two areas: ecological biogeography, which is concerned with current distribution patterns, and historical biogeography, which is concerned with long-term and large-scale distributions. if evolution were in fact the case, we should generally expect species that are closely related to be found near each other, unless there are good reasons for them not to be, such as great mobility (for example, sea animals, birds, and animals distributed by humans, or over longer time frames, plate tectonics). If, however, we found that species were distributed in an effectively random geographic manner, with closely related species no more likely to be located close to each other than not, this would be strong evidence against evolution and common descent. If life forms arose independently, for example, it would make as much if not more sense for them to exist wherever an environment could support them, as opposed to being distributed according to their apparent relationship to other life forms. -the study of the distribution of life forms over geographical areas.

Disruptive Selection

the two sides of the bell curve is favorable but the middle is not.

Speciation

the two species flowers, Aquilegia formosa (red and yellow in low elevations) and Aquilegia pubescent, were different at the ends of the elevational ranges. This is an example of speciation that is still not completed as the individuals in the middle of the mountain range are still interbreeding. When the trait values become so different that this is no longer possible, selection may result in two species that have two types of flowers. So, when the two populations can not interbreed naturally to give rise to viable offspring they become species. With time, selective forces bring evolutionary change that produces two or more separate species. This is called speciation, and it is represented as the branching points on the phylogenetic tree. For speciation to occur, there needs to be a genetic difference between two populations that prevents their mating and reproduction. A good example of such genetic changes is the single amino acid difference in the chestnut belly flycatcher (Monarcha castaneiventris) in the Solomon Islands that transformed it into a completely black subspecies -when two populations can no longer interbreed naturally and give rise to viable offspring which causes them to become species.

Effectiveness of Stem Cell Therapy

we do not know yet. The only concrete example of successful stem cell therapy so far is bone marrow transplantation, which has been used for 40 years to treat leukemia, immune system disorders, and other blood-related diseases. Bone marrow transplants repopulate a patient's defective or destroyed marrow with adult hematopoietic stem cells, which are able to form every type of blood cell. Other therapies using adult stem cells are currently in clinical trials, but none have been approved for general use. Embryonic stem cell therapies are even further behind. The very characteristics that make stem cells useful - self-renew and pluripotency - could also be a major problem during treatment. If some of the injected cells do not follow their differentiation path, they could grow uncontrollably into a tumor. This is a major concern for ES cell therapy that is currently being addressed. Another problem facing stem cell therapies is genetic compatibility. As with bone marrow transplants, stem cell treatments may need to be a genetic match. In the case of a non-match, the patient could reject the injected cells, or the cells could mount an immune response against the patient as in graft versus host disease. The recent success of iPS cells may help circumvent this problem by generating patient-specific stem cell therapies. A patient would have a skin biopsy, the cells would be dedifferentiated in the laboratory into iPS cells, which could then be used to generate any given stem cell treatment. Since the cells originally came from the patient himself, the treatment would be an identical genetic match!

Sexual Selection

when selection happened due to mating preferences -a natural selection in which certain traits on a male or female are favorable and attract a mate insuring that the favorable trait is passed down.

Peter and Rosemary Grant

worked out of Princeton, picked one little tiny island among the Galapagos called Daphne Major. This island is small enough so that they could catch and mark every single bird on the island. They showed that every part of natural selection is operating on this island. They demonstrated that variation exists in Geospiza fortis finches. Among the population there were 751 birds and these birds varied in how big their bill was. This would be a roughly normal distribution. We would get the same distribution if we graphed human height within a population.

Feedback Loops and Gene Expression

you can think of gene expression as a simple feedback loop. We will first go over two very simple feedback loops, and then describe a more detailed feedback loop. Remember the structure of a gene with the promoter region before the open reading frame. Well, the promoter controls gene expression. The promoter tells the system whether or not to start transcription. A NEGATIVE feedback loop: the promoter tells transcription to begin. After the mRNA is made, the transcript is translated into protein. The presence of the protein (represented by the line) tells the promoter to stop transcription. Because the protein is present, the cell no longer needs to make additional protein, so transcription is stopped. A POSITIVE feedback loop of transcription: the presence of the protein actually activates transcription and tells the promoter to turn transcription on.