Unit 1 Evaluation

1. What were the three aspects of the assignments I've submitted that I am most proud of?
I really enjoyed searching the internet for more information and finding interesting links and photos to add to my compendiums.
I spent alot of time on the entire unit completing the assignments and trying to learn all of the information.
I learned how to use Google Notebook. :) Thanks!

2. What two aspects of my submitted assignments do I believe could have used some improvement?
I need to be more precise with my compendiums.
I need to spend more time on the web links. There is a wealth of information there.

3. What do I believe my overall grade should be for this unit?
A

4. How could I perform better in the next unit?
Well I certainly learned that taking written notes while I read the first four chapters is not efficient. On the second major topic, I started writing my compendium while I read. That worked well. Now I want to continue to tweak and improve my compendiums.

Cell Metabolism & Gene Function: Unit 1 Lab Project

Introduction
The assignment for our first Lab Project was to build a model of cell.
First I will list the parts of the cell represented in the first section and the function of each. Then I will go through each picture that I took and explain which item is representing each part of the cell.

For the DNA replication, transcripton and translation, my representations varies slightly from my cell model, so I will display addtional pictures that walk through those functions explaining how each component is represented as I go.

List of Cell Parts with Functions
Cell (plasma) membrane - The selectively permeable outer boundary of the cell. It separates the inside of the cell from the outside of the cell and regulates what goes into and out of the cell.
Nucleus - Stores the genetic material. Location of DNA replication and transcription.
Nuclear membrane - Double membrane that separates the contents of the nucleuls from the cytoplasm.
Nuclear pores - Allow movement of ribosomal subunits out of the nucleus and proteins into the nucleus.
Endoplasmic reticulum (ER) - Rough ER is studded with ribosomes on the cytomplas side. After production at the ribosomes, proteins enter the rough ER interior for processing and modification. Smooth ER produces phosolipids. There are no ribosomes on the smooth ER.
Golgi apparatus - Receives proteins and phosolipids from the ER for modification.
Lysosomes - Produced by Golgi apparatus. They fuse with endocytic vesicles, digest the contents, and release them into the cytoplasm.
Vesicle - Membrane-bounded sac that stores and transports different substances.
Mitochondria - The powerhouse of the cell. Produces ATP through the process of cellular respiration.
Microtubule - Part of cytoskeleton. Provide support and aid in movement of organelles around the cell.

Description of Model
I started with a bucket covered with material that was white with gold starts for the nucleus. The material represents the nuclear membrane and the gold stars represent the nuclear pores. The nucleus is sitting on top of a half basket, which represents the plasma membrane (the plasma membrane is labeled in a later photo). Next I added the endoplasmic reticulum. For this I used a wide piece of ribbon and used gold beads to represent the ribosomes that stud the rough endoplasmic reticulum. The smooth endoplasmic reticulum is represented by the area of ribbon without the gold beads. The Golgi apparatus is represented by the blue jean material. Next, I added the lysosomes and vesicles which are represented by the clear, red, and pink beads. For the microtubules I used pipe cleaners, and for the mitochondria I used gold ornaments.Lastly, a picture of the entire cell, showing all of the parts described above.

DNA Replication, Transcription, and Translation
A few additional molecules are required to explain these processes.
Chromosome - DNA in a condensed form. When the DNA is in this compact form, it means they have been duplicated and are ready for mitosis or meiosis.
mRNA - DNA is transcribed into mRNA, which then takes the gentic code to the cytoplasm for translation.
rRNA - Combine with proteins to form ribosomes, which are the location of protein synthesis.
tRNA - Carry anticodons and amino acids to mRNA to aid in protein synthesis.
Ribosomes - Composed of rRNA and proteins; location of protein synthesis.

The nucleus is now represented by the half basket. The gold ribbon with green stripes are the chromosomes. The vertical edges of the ribbon represent the sugar phosphate backbone of the DNA double helix, and the green stripes represent the complementary bases.
This picture shows DNA replication. The double helix has unzipped and two new strands of DNA are being formed as complementary bases of the new strand bond with the bases of the original strand.
Next up is DNA transcription. Here you can see the DNA double helix unzipped at the location of transcription. A mRNA molecule is formed as complementary bases line up with one strand of the DNA. The mRNA is represented by the bold ribbon with the red backbone.
Translation is represented in the last photo. The ribosomal subunits have binding locations for both the mRNA and the tRNA. The codon of the mRNA dictates which tRNA will bond next. There is a specific anticodon on the tRNA that will bind with the corresponding codon of the mRNA. On the other end of tRNA is an amino acid. The polypeptide chain grows as the subunit moves along the mRNA.
Conclusion
Through this lab project, I assembled a large scale model of a cell that included the nucleus and nuclear membrane, the ER, the Golgi apparatus, the mitochondria, and the microtubules, lysosomes, and vesicles. I later constructed a model that represented DNA replication, transcription and translation. This assignment held solidify in my mind what all of these parts of the cell do. I can better visualize both the parts and the processes in my mind.

Unit 1 Ethical Issue: Genetic Technologies

Pass the Corn Please

Genetic engineering is the altering of genetic material. The purpose of genetic engineering is to produce a new, a better, or more of a "product." The "product" can be anything from insulin, to a salt-tolerant tomato plant, to a new liver. At the heart of genetic engineering is recombinant DNA. Recombinant DNA contains DNA from two or more different sources. To create it, scientists find a gene that has the characteristics that they are looking for, they cut out that segment of DNA, join it to a plasmid, and insert the plasmid into a host cell. As the host cell divides, the gene of interest is cloned, and you end up with, among other things genetically modified food. There exist both benefits and drawbacks over the use of genetic engineering in general, and more specifically over the use of its products in our farmlands, which ends up on our tables.

The benefits of growing genetically modified plants are numerous. Scientists have developed plant varieties that are resistant to herbicides. The benefit of this to the farmer is that weeding is not required and sometimes only one herbicide is required. What this means is that the farmer does not need to till, which contributes to soil erosion, and only one application of a herbicide is required instead of the application of multiple herbicides. Other plant varieties have been engineered to tolerate cold temperatures to prevent the devastating effects of frost. Plant varieties are also being engineered for improved nutrition. For third world countries that rely on one crop as their main source of food, improved nutritional value per serving could help reduce malnutrition.

At the other end of the spectrum is another view of the use of genetic engineering as it relates to our food supply. One of the biggest concerns is about the safety of the food that is produced. In general, there is concern that there is no way to know which products at the grocery store contain genetically modified foods and which do not. Many also believe that genetically modified foods may introduce new allergens, especially in children. Others worry over the impact to the environment. The pest resistant varieties of plants that are being developed could also be inadvertently killing other organisms, along with the pests. It may also be possible for the gene to transfer to other plant species. For instance the herbicide resistant gene could be transferred from the target crop into a weed species. This could make that weed tolerant to the same herbicide.

As you can see, there are valid arguments both for and against the use of genetically modified plants in the food supply chain. There are benefits that range from reducing erosion to improving nutritional value. The biggest arguments against their use are the potential health risks and the potential impact to the environment.

I believe that this argument will continue for some time to come. Research will continue; new variations will be developed and tested. Tests and studies will continue to determine if any concerns are legitimate. Labeling will be improved, so that people will have the option of choosing genetically modified food or choosing non-genetically modified food. Profit, in the end, will determine whether the use of genetically modified plants continues.

Gentics: Online Lab #2

The human genome is made up of 15,000 genes that exist on 23 pairs of chromosomes. Each parent contributes one of each chromosome to their offspring. It is our genes that dictate so much of who we are today. Everything from the length of our fingers, to the color of our eyes, to whether or not certain protein receptors in our plasma membrane work correctly is determined by our genes. The variations that exist for any given gene are called alleles. Although both parents pass on to us one of every gene, not every allele that we receive is expressed as a trait in our phenyotype. In order for a recessive allele to be expressed, a person must receive the recessive allele from both their mother and father. If one dominant allele is received, the dominant phenotype will prevail.

When looked at from an evolutionary perspective, the genes we have today were "selected" for by nature. They provided our ancestors some advantage over others, such that they were able to reproduce and pass on those genes.

The purpose of this lab was to confirm my understanding of how genes are inherited and how those genes affect the adult phenotype.

First, I will start with the definitions.
1. Genotype - the genes of an individual. When looking at one trait that is coded for by one set of alleles, the genotype is represented by 2 letters. One letter stands for the allele received from the mother, the other letter represents the allele received from the father. For instance, in the case of the fruitfly, the 3 genotypes in scenario 5 were Ll, LL, and ll.
2. Phenotype - the physical appearance of the trait that is expressed through the genotype. Back to the fruitfly, the 2 phenotypes that could be expressed by the 3 genotypes are as follows: LL=long-winged, Ll=long-winged, ll=vestigial-winged.
3. Allele - variations of the same gene. A few examples of alleles from dragon lab are horns vs no horns, wings vs no wings, scales vs no scales. There are dominant alleles and recessive alleles. If an individual has at least one copy of the dominant allele, the dominant allele will be expressed. For the recessive allele to be expressed, the individual must have both copies of the recessive allele. (Unless it is an x-linked allele in males) The alleles for a given trait occur at the same loci of homologous pairs.
4. Cross - refers to taking the genotype of a set of parents and determing the possible genotype/phenotype of their offspring through the use of a Punnett Square. For example, in scenario 5, we crossed a heterozygous long-winged fly (genotype=Ll) with a heterozygous long-winged fly (genotype=Ll).
5. Dominant - when referring to genes and alleles, the dominant allele is one that will express itself any time it is present. In other words, the dominant allele will express itself in the heterozygous individual (1 copy of dominant allele, 1 copy of recessive allele) or in the homozygous dominant (2 copies of dominant allele) individual. In the scenario 5, the dominant allele is long wings. Both parents were heterzygous for this trait. Both had long wings because they each had one copy of the dominant long-wing allele.
6. Recessive - when referring to genes and alleles, the recessive allele is one that will only be expressed in the individual if both copies are present. In the fruitfly lab, the vestigial-wing was the recessive allele. The vestigial-winged fruitfly has 2 copies of the recessive allele for the vestigial-wing.

Here is the screen shot from the dragon lab. In this lab I had to change the genotype (to the right of the dragons) of the second dragon so that its phenotype (physical apperance) matched that of the first dragon.

Here is the screen shot from the Punnett Square lab. This shows the offspring that could result from the crossing of two heterozygous long-winged parents. This visuals shows both the genotype and the phenotype for each individual.

Hair color. Hairline. Eye shape. Eyelash length. Freckles. Ability to roll your tongue. All of these things are human traits that are coded for in an individuals genes, all of which are passed down from the parents. Each parent supplies half of an individual's genome. This is possible through the process of meiosis. Meiosis includes 2 phases of nuclear division. It is the 2 phases of nuclear division that allow the gametes to end up with half the genetic information of the parent cell. The first phase separates the homologous pairs into two daughter cells, and the second separates the sister chromatids. In this way, the gamete ends up with only half the genetic information of the parent cell. The full genome is restored once a sperm cell and egg cell join during fertilization. It is the combination of genes that make up who we are. The combination is also what provides for so much variation between individuals.

Compendium Review Unit 1 Major Topic: Genetics

GENETICS
I. PATTERNS OF CHROMOSOME INHERITANCE
A. Chromosomes and the Cell Cycle
1. Humans - 46 chromosomes, 23 pairs
2. Karyotype - total view of all 23 pairs
3. 1 pair is sex chromosomes
4. The cell cycle
a. interphase (G1, S, G2 stages) normal functions, getting ready to divide, DNA synthesis
b. cell division - mitosis and cytokinesis
From the text, figures 18.1, showing the karyotype of a male, and 18.2 illustrating the cell cycle.B. Mitosis (for growth, replacement, repair; constant)
1. Prophase
a. chromosomes condense, visible
b. nuclear envelope fragments
c. nucleolus disappears
d. centrosomes move to opposite ends the nucleus
e. spindle fibers appear and attach to centromere
2. Metaphase
a. chromosomes line up along equator of the cell
b. fully formed spindle
3. Anaphase
a. centromeres split
b. sister chromatids separate (now chromosomes)
c. chromosomes move toward opposite poles of spindle
4. Telophase
a. chromosomes arrive at poles
b. chromosomes -> indistinct chromatin
c. spindle disappears
d. nucleoli reappear
e. nuclear envelope reassembles
5. Cytokinesis (split - cytoplasm & organelles, cleavage furrow)
Figure 18.3 from the text provides a nice overview of mitosis.
C. Meiosis (haploid gametes, 2 nuclear divisions)
1. Meiosis I (prophase I, metaphase I, anaphase I, telophase I)
a. synapsis and crossing-over - prophase I
b. homologous pairs align independently at equator - metaphase I
c. homologous pairs separate - anaphase I
c. 2 haploid daughter cells - telophase I
2. Meiosis II (prophase II, metaphase II, anaphase II, telophase II)
Figure 18.7 from the text provides a nice overview of meiosis.
D. Spermatogeneis (production of sperm in males)
1. Primary spermatocyte 2n(meiosis I)
2. 2 secondary spermatocytes n (meiosis II)
3. 4 spermatids n
4. After puberty, continual, 300k / min
E. Oogenesis (production of egg in females - meiosis and maturation)
1. Primary oocyte 2n (meiosis I)
2. Secondary oocyte n and first polar body n
3. Secondary oocyte stops meiosis II at metaphase II
4. Travels to oviduct, completes meiosis II only if fertilized
F. Fertilization
1. Steps
a. sperm swims with flagellum
b. only 1 sperm enters egg,
c. only sperm nucleus fuses with egg nucleus (cytoplasm and organelles from mother)
G. Pre-Embryonic and Embryonic Development
1. Processes of development (cleavage, growth, morphogenesis, differentiation)
2. Extraembryonic membranes (chorion, placenta, allantois, yolk sac, amnion)
3. Stages of development (fertilization to birth)
a. pre-embryonic development (fertilization to appearance of chorion)
b. embryonic development (implantation to eighth week)
Figure 17.3 from the text illustrates pre-embryonic development. Figure 17.4 illustrates embryonic development.
G. Chromosome inheritance
1. Trisomy, monosomy caused by nondisjunction
2. Down Syndrome - autosomal trisomy
3. Changes in sex chromosome #s - Turner, Klinefelter, Jacobs, Poly-X Female
4. Changes in chromosome structure
a. deletion - Williams syndrome, Cri du chat (cat's cry)
b. duplication
c. inversion
d. translocation - Alagille syndrome
II. CANCER
A. Cancer Cells
1. Characteristics
a. lack differentiation (not specialized - epithelial, muscle, nervous, connective)
b. have abnormal nuclei
c. have unlimited ability to divide (telomerase gene turned on)
d. form tumors (no contact inhibition)
e. divide without growth hormones
f. become abnormal gradually (carcinogenesis)
g. undergo angiogenesis and metastasis
2. Cancer is genetic
a. proto-oncogenes become oncogenes
b. tumor-suppressor genes become inactive
3. Types of Cancer (see definition page - sarcomas, lymphomas, carcinomas)
Figure 19.2 illustrates the progression of the tumor.B. Causes
1. Heredity - BRCA1, BRCA2, RET, RB
2. Environmental carcinogens
a. radiation - UV light, X-rays, radon gas
b. organic chemicals - tobacco smoke, pollutants
c. viruses - HepB & C, Epstein-Barr, human papillomavirus
C. Diagnosis
1. Seven warning signs
a. Change in bowel or bladder habits
b. A sore that does not heal
c. Unusual bleeding or discharge
d. Thickening or lump in breast or elsewhere
e. Indigestion or difficulty swallowing
f. Obvious change in wart or mole (ABCD)
g. Nagging cough or hoarseness
2. Routine screening
a. Self-exam (breast and testicle)
b. Colonoscopy
c. Mammogram
d. Pap smear
e. PSA
3. Tumor marker tests - blood tests for tumor antigens/antibodies
4. Genetic - test for mutations in proto-oncogenes and tumor-suppressor genes
The image below shows the crystal structure of the human hepatitis B virus capsid. The reference can be found here.D. Treatment
1. Standard therapies
a. surgery
b. radiation - localized therapy, causes chromosomal breakage, disrupts cell cycle
c. chemotherapy - treats the whole body, damages DNA, interferes with DNA synthesis
d. bone marrow transplant
2. New therapies
a. immunotherapy
b. p53 gene therapy
III. PATTERNS OF GENETIC INHERITANCE
A. Genotype and Phenotype
1. Genotype - genese of an idividual
2. Phenotype - visible expression of a genotype
B. One- and Two-Trait Inheritance
1. Forming the gametes
a. gametes carry half the chromosomes
b. gametes carry allele for each trait
2. One-trait crosses (Punnett square, genotypic and phenotypic ratios, probability)
3. Two-trait crosses (dihybrid cross, probability)
4. Family pedigrees for genetic disorders
5. Genetic disorders of interest
a. Autosomal recessive (Tay-Sachs, CF, phenylketonuria, sickle-cell disease)
b. Autosomal dominant (Marfan syndrome, Huntington disease)
Figure 20.6 from the text shows the resulting offspring when crossing two dihybrids. C. Beyond Simple Inheritance Patterns
1. Polygenic inheritance (polygenic traits=>continuous variation of phenotypes)
a. dominant allele codes for a product
b. skin color
c. multifactorial disorders - controlled by polygenes that are subject to environmental influences (Himalayan rabbits)
2. Incomplete dominance (wavy hair) and codominance (AB blood type)
3. Multiple allele inheritance (ABO blood types)
D. Sex-Linked Inheritance
1. X-linked alleles
a. in males, always inherited from mother
2. Pedigree for X-linked disorders
a. recessive disorders more often expressed in males b/c the Y chromosome lacks the allele
b. color blindness
c. muscular distrophy
d. hemophelia
Figure 20.18 from the text shows the pedigree for color blindness and lists ways in which to recognize a recessive X-linked disorder.IV. DNA BIOLOGY AND TECHNOLOGY
A. DNA and RNA Structure and Function
1. Structure of DNA
a. double helix
b. 2 backbones - sugar-phosphate
c. complementary base pairs = "ladder rungs" (purines=AG, pyrimidines=TC)
2. Replication of DNA
a. process of copying a DNA helix
b. double helix unwinds and unzips, each is a template (semiconservative)
c. complementary base pairing
d. 2 identical double helices produced
3. Structure and function of RNA (A,U,G,C)
a. rRNA - produced in nucleus, joins w/proteins to form subunits of ribosomes
b. mRNA - produced in nucleus, carries genetic info from DNA to ribosomes
c. tRNA - produced in nucleus, transfers amino acids to ribosomes
Figures 21.2 and 21.3 from the text show how, during replication, DNA is unzipped and new complementary bases of the nucleotides pair up to the old strand.
B. Gene Expression
1. Structure and function of proteins
a. made of 20 different proteins
b. determine structure and function of cells in our body
2. Transcription (nucleus)
a. section of DNA is template for production RNA molecule
b. resulting RNA has sequence of complementary bases and U takes the place of T
3. Translation (cytoplasm)
a. tRNA molecules contain anticodons, complementary to codons on mRNA
b. tRNA contains amino acid at other end
c. order of condons on mRNA dictate order of tRNA amino acids
d. occurs at ribosomes
4. Regulation of gene expression (not all genes on all the time)
a. transcriptional control - in nucleus, chromatin density and transcription factors
b. posttranscriptional control - in nucleus, mRNA processing
c. translational control - in cytoplasm, differential ability of mRNA to bind to ribosomes
d. posttranslational control - in cytoplasm, changes to the protein to make it functional
Figures 21.11 and 21.13 from the text illustrate the process of polypeptide synthesis and and overview of gene expression.
C. Genomics
1. The human genome has been sequenced - order of 3 billion base pairs, 25k genes
2. Functional and comparative genomics - how do our genes function, how do they compare to other species?
3. Proteomics and bioinformatics
4. A person's genome can be modified (ex-vivo & in-vivo gene therapy)
D. DNA Technology
1. Genes can be isolated and cloned (recombinant DNA)
2. Specific DNA sequences can be cloned (polymerase chain reaction)
3. Biotechnology products / genetic engineering
a. bacteria - insulin, human growth hormone, hepB vaccine
b. plants - insect and herbicide resistant, salt-tolerant plants
c. animals - bovine growth hormone, gene pharming, xenotransplantation
The photograph below is of Dolly, the first cloned mammal. I. PATTERNS OF CHROMOSOME INHERITANCE
Mitosis and meiosis - very similar, yet very different processes. To start, here is a fun animation along with a real life video that walks through the steps of mitosis. On the same website is an animation for meiosis. You can either play the video straight through or use the step buttons to walk through each phase. I am going to walk through a few of the differences between mitosis and meiosis. First, in meiosis, there are two nuclear divisions whereas in mitosis there is only one. That means that meiosis produces four daughter cells and mitosis produces only two. The four daughter cells from meiosis are haploid cells and the two daughter cells from mitosis are duploid. The daughter cells from meiosis are not genetically identical to the parent cell; they only have half the number of the parent cell. The daughter cells from mitosis are genetically identical to the parent cell. Meiosis occurs in sex cells and the purpose of it is to produce gametes. Mitosis occurs in automsomal cells and the purpose of it is for growth, for replacement and for repair. (Mader 2008)

Definitions for chapter 18 can be found here.

II. CANCER
In 2005, cancer was the #2 leading cause of death in the US. With statistics like that, it seems like a no brainer - put into practice the recommended preventions of cancer. The text breaks down the list into two sections: Protective Behaviors and The Right Diet. A few behaviors one can change to help prevent cancer are to avoid smoke/smoking, avoid the sun and tanning beds, avoid alcohol and radiation, and be aware of occupational hazards. Many studies show that following a certain diet can also help in the prevention of cancer. Things like avoiding obesity, eating plenty of high-fiber foods, increasing consumption of foods rich in vitamins A & C, and including vegetables from the cabbage family in the diet. The American Cancer Society is a great resource for more information on prevention and detection.

Definitions for chapter 19 can be found here.

III. PATTERNS OF GENETIC INHERITANCE
Sex-linked inheritance is different from autosomal inheritance in that male offspring only receive one allele for a given trait. That allele is passed to them from their mother. The Y chromosome that he received from his father does not carry an allele for that trait. In this way, males have a 50% chance of inheriting an X-linked recessive disorder if their mother is heterozygous. If he inherits the recessive allele from her, it will always express itself, since that is the only allele for that gene he will receive. The case is different for the daughter, who, without an affected father, has a zero percent chance of inheriting the disorder. She does, however, have a fifty percent chance of being a carrier. (Mader 2008)

Definitions for chapter 20 can be found here.

IV. DNA BIOLOGY AND TECHNOLOGY
Transcription and translation. This is another area of biology that has me in complete amazement. The fact that we understand how our genes are copied and translated into proteins...the idea renders me speechless. And here it, my general overview. Transcription is the process by which a segment of RNA is made from a segment of DNA. The portion of the double helix that is to be transcribed unwinds and unzips so that the "ladder rungs" or bases are exposed. The exposed bases allow the complementary base pairs that will join to form RNA to line up in the correct order. RNA polymerase joins the nucleotides together to form RNA. rRNA, mRNA, and tRNA are all made in the nucleus in the same way. After production and processing, the 3 types of RNA move to the cytoplasm. mRNA finds the ribosomes (rRNA plus proteins) where translation occurs. Translation is the production of a polypeptide chain; the order of the amino acids in the chain is determined by the order of condons on mRNA. Codons are made up of three bases on mRNA. A codon of mRNA will only bind with the corresponding anticodon of tRNA. Each anticodon correlates to an amino acid that tRNA also carries. As mRNA moves through the ribosome, the codons pair with anticodons. The amino acid that was associated with that anticodon on tRNA gets added to the polypeptide chain. In this way, mRNA dictates the order of amino acids in a polypeptide chain.

Chapter 21 definitions can be found here.

REFERENCES:
Mader, Syliva S. Human Biology. New York, NY: McGraw-Hill (2008).

Links provided throughout the summary take you to online sources.


IMPORTANT NOTE: Any time "text" or "the text" is referenced in the above summary, I am referring to the textbook Human Biology by Sylvia Mader (cited directly above).

Compendium Review Unit 1 Major Topic: Cells

CELLS
I. BASIC CHARACTERISTICS OF LIFE
A. 7 Characteristics
B. Humans are related to other animals
C. Science and social responsibility
II. THE CHEMISTRY OF LIFE
A. What are molecules made of?
B. Importance of water
C. Carbohydrates
D. Lipids
E. Proteins
F. Nucleic acids
III. CELL STRUCTURE AND FUNCTION
A. The fundamental unit of life
B. Ancestors of animal cells
C. The gate
D. The control center
E. The infrastructure
F. The powerhouse
IV. TISSUE TYPES AND HOMEOSTASIS
A. Supports and connects
B. Moves and beats
C. Sends, receives and processes
D. Protects
E. The goal of organ systems

THE BASIC CHARACTERISTICS OF LIFE
One of the main points that I have learned from this unit is that life has evolved. The fact that the characteristics of life can be compiled into a short list of seven helps one to understand that all living things were created from the same single cell. It is mind-boggling: Every living thing on this Earth can be identified as living by only seven characteristics. And those 7 characteristics are that living things: 1. Are organized, 2. Take materials and energy from the environment, 3. Reproduce, 4. Grow and develop, 5. Are homeostatic, 6. Respond to stimuli, 7. Have an evolutionary history (Mader 2008). Figure 1.2 from the text (Mader 2008)does a great job in showing how life is organized all the way from an atom up to the Earth's biosphere. The idea of how acquiring materials and energy is needed by all living things can be understood by looking at humans and food intake. Humans eat for many reasons, but the actual need is at the cellular level. Cells need nutrients from food to produce the energy to run the processes that keep them alive. The same is true of a single celled prokaryote. One goal of all living things is to reproduce or to pass on their genes to the next generation. Once a new organism is produced, it must grow and develop so that it can also take in materials, produce energy, and eventually pass on it's genes as well. Along the way, it must maintain homeostasis, so that all of the processes required to produce energy, to grow, to develop, and to reproduce and run normally. If homeostasis is not maintained, proteins will break down, processes will cease, and the internal systems will stop functioning properly. Linked closely to homeostasis is the ability to respond to stimuli. As an organism's outside environment changes, it needs to be able to make adjustments that allow it to maintain homostasis. In order to do this the organism must have a way of notifying its internal systems and then make changes accordingly. And lastly, evolution "explains both the unity and the diversity of life. All organisms share the same characteristics of life because their ancestry can be traced to the first cell or cells. Organisms are diverse because they are adapted to different ways of life" (Mader 2008).

Over time, scientists have developed a classification system into which all organisms can be placed. Taxonomy is built upon the basic fields of morphology, physiology, ecology, and genetics (source1). The system starts with the 3 very broad domains. They are the Eukarya which have a membrane-bounded nucleus and the Archaea and Bacteria which both lack a membrane-bounded nucleus. Within the domain Eukarya are the four kingdoms Animalia, Plantae, Fungi, and Protista. Humans are mammals in the vertebrate class which is part of the kingdom Animalia. Humans are distinguished from other Eukaryotes because we have a nerve cord that is protected by a vertebral column which has repeating units. This indicates that we are segmented animals (Mader 2008).

Part of what separates humans from other mammals also makes us dangerous to our biosphere. We have highly developed brains, we use creative language and we have the ability to use a wide variety of tools. Among others, these factors have allowed us to continue to make significant technological advances over the course of our history. While many of these discoveries have enriched our lives, many have also negatively impacted our environment. Humans are constantly modifying our environment and impacting the biodiversity of our planet.

As mankind continues to make exciting new advances, it becomes increasingly more important for everyone to be educated and take a stand on the ethical issues that these new advances bring to light.

THE CHEMISTRY OF LIFE
Molecules, although small in size, can be broken down into even smaller parts. Learning a few basic definitions in chemistry will help to explain this. Matter is anything in this world that has mass and takes up space. It refers to living organisms as well as inanimate objects. One of the basic building blocks of matter then is the element and the smallest unit of an element is the atom. Atoms are made up of protons, neutrons, and electrons. Protons carry a positive charge, electrons carry a negative charge, and neutrons are electrically neutral. The protons and neutrons are located in the nucleus of the atom and the electrons circle the nucleus in electron shells. Atoms are most stable when their outer shell is filled with 8 electrons. Electrons in the outer shell can be shared with other atoms (covalent bonding) or one atom may give up an electron and another atom can accept it (ionic bonding). These two types of bonds are what allow atoms to form molecules and compounds.

One very common compound is water, which is made up of two hydrogen atoms and one oxygen atom. The 6 electrons in the outer shell of the oxygen atom and the 2 electrons (total) from the 2 hydrogen atoms bond covalently to fill the outer shell of each atom. The oxygen atom, because it is a larger atom, has a greater ability to attract the electrons towards it. This causes the water molecule to be polarized, meaning the oxygen side of the molecule has a slightly negative charge and the hydrogen side of the molecule has a slightly positive charge (Mader 2008). Because of this polarity, the hydrogen side of the molecule is attracted to a negatively charged atom, even at some distance away. This attraction is called a hydrogen bond (Mader 2008). Figure 2.7 from the text illustrates the polarity how the polarity of water allows hydrogen bonds to form.The polarity and hydrogen bonding are what allow water to have the following crucial characteristics that are so important to life. 1. Water is liquid at room temperature, so we can drink it. 2. The temperature of liquid water rises and falls slowly, preventing sudden or drastic changes. 3. Water has a high heat of vaporization, keeping the body from overheating. 4. Frozen water is less dense than liquid water so ice floats on water. 5. Water molecules are cohesive, so liquids fill vessels such as blood vessels. 6. Water is a solvent for polar molecules, and thereby facilitates chemical reactions both outside and inside of our bodies (Mader 2008).

Cells in every living organism are composed of four organic molecules or molecules that contain carbon and hydrogen. They are carbohydrates, lipids, proteins, and nucleic acids. When a cell builds or breaks down organic molecules, it uses a dehydration reaction and hydrolysis reaction, respectively. A dehydration reaction removes a hydroxyl group (-OH) and a hydrogen atom (-H) from the subunits that are involved to form the molecule. A water molecule is also formed. A hydrolysis reaction takes a water molecule and adds it back (in the form of a hydroxyl group and a hydrogen atom) to the subunits of the molecule to break it down (Mader 2008).

The first of the four molecules of life is the carbohydrate. Carbohydrate molecules are characterized by the presence of the atomic grouping H-C-OH in which the ratio of hydrogen to oxygen is approximately 2:1. Their purpose is for quick and short-term energy storage in all organisms (Mader 2008). Carbohydrates range in structure from simple to complex. Simple carbohydrates or simple sugars are those that have from 3 to 7 carbon atoms. A disaccaride is also considered a simple sugar. It consists of 2 monosaccarides that have joined together by dehydration. Complex carbohydrates or polysaccharides are macromolecules that contain many glucose units joined together. A few examples of polysaccharides are starch, glycogen, and cellulose (Mader 2008).

The second molecule of life is the lipid, another energy storage molecule, but energy storage is not their most significant function. The most important characteristic of lipids is that they do not dissolve in water because, in general, they are not polarized. Lipids are found as fats and oils, as steroids, and as phospholipids. These three groups of lipids differ from each other in structure and function. When 3 fatty acids (molecule of a carbon-hydrogen chain that ends with the acidic group -COOH) combine with 3 molecules of glycerol by dehydration, a fat molecule and 3 water molecules are produced (Mader 2008). In the body, fat molecules are used for long-term energy storage, insulation, and cushioning. Steroids, on the other hand, are molecules that have a backbone of four fused carbon rings. Steroids differ from each other based on functional groups that are attached to the backbone. One example of a steroid is cholesterol which serves as a component of the plasma membrane in animal cells and is also the precursor to other steroids (Mader 2008). The last group of lipids is the phospholipids. Phospholipids are made up of two fatty acids and a phosphate group. The fatty acids are nonpolar and are therefore hydrophobic. The phosphate group is ionized and is therefore hydrophilic. It is the structure of the phospholipid that allows it to carry out what could arguably be the most significant function that lipids do. The hydrophobic tails and the hydrophylic heads form a bilayer in watery solutions. The tails face towards each other and the heads face the solution. In this way, phospholipds form the plasma membrane of every living cell. The pictorial below taken from this website shows how the phospholipid bilayer can form a plasma membrane.
The third molecule of life is the protein. Proteins have many functions, such as providing structural support, catalyzing reactions, transporting substances into and out of the cell, protecting the body by 'attacking' antigens, regulating homeostasis, and causing muscles to contract (Mader 2008). Proteins are made up of subunits called amino acids. An amino acid is made up of a carbon atom that is bonded to a hydrogen atom, an amino group, a acid group and an R group. Amino acids are joined together through peptide bonds. The linear sequence of peptide bonds (polypeptide )is what constitutes the primary structure of the protein. There are at least two and sometimes three additional levels of organization that define a protein. The secondary structure is the orientation that the polypeptide takes on. There are two types: the alpha helix or the pleated sheet. The tertiary structure of a protein is its final three-dimensional shape. Whatever the final shape may be, the hydrophobic sections stay towards the inside while the hydrophilic sections stay towards the outside. When two or more polypeptides join together, the quaternary structure is formed. Not all polypeptides join with others to for the quaternary structure. Figure 2.20 from the text provides an overview of each level.The folding of amino acids into proteins is one area that remains a mystery to scientists. For the most part, they have not been able to figure out why a protein folds up the way it does. Much time, energy and resources have been and still are being put into this field of biology. One example is the Blue Gene project out of IBM and another is the Folding@home, distributed computing project out of Stanford University. This area of study is so important to the understanding, treatment, and possible prevention of many diseases that develop when a protein does not fold up correctly.

Last but not least in the list of molecules of life are the nucleic acids. DNA and RNA are the two types of nucleic acids. The difference in structure between the nucleotides of the two is essentially given in their names. DNA stands for deoxyribonucleic acid and the pentose sugar that it contains is deoxyribose. RNA stands for ribonucleic acid and the sugar that it contains is ribose. The nucleotides of DNA and RNA each also contain a nitrogen-containing base and a phosphate. There are four types of bases in DNA: adenine, thymine, guanine, and cytosine. In RNA uracil replaces thymine (Mader 2008). The other 3 bases are the same. The sugar of one nucleotide bonds with the phosphate of the next to form the backbone of polynucleotide strand (Mader 2008). In DNA, two strands bond via hydrogen bonds between the bases to form a double helix. The same bases always pair together (complementary base pairing): A-T and G-C (Mader 2008). Complementary base pairing allows DNA to replicate in a way that ensures the sequence of bases will remain the same (Mader 2008). It is the sequence of bases that determine the sequence of amino acids in a protein (Mader 2008). RNA is single stranded and forms through complementary base pairing with DNA (Mader 2008). Nucleic acids are also involved in cell metabolism. ATP is adenosine plus three phosphate groups. The first image shown below taken from the text shows the 3 subunits of a nucleotide. The image below it, figure 2.21 from the text, shows the sugar phosphate backbone plus complementary base pairing of DNA.
CELL STRUCTURE AND FUNCTION
The cell theory tells us 3 things: 1. A cell is the basic unit of life, 2. All living things are made up of cells, 3. New cells arise only from preexisting cells. There is much depth behind these three seemingly simple statements. What you can take from these three statements is that the fundamental unit of life, the cell, connects us to all other living things. It is a mind boggling concept. The development of the compound microscope played a huge role in the discoveries that led to the development of the cell theory. In addition to the 2 dimensional, magnified views that the compound microscope provides, scientists today can also view a magnified 3d image of the surface of an object with the use of a scanning electron microscope. Although the image seen with the use of a transmission electron micrscope is only 2d, the magnification power and resolving power are much greater than those of a compound light microscope.

Before diving into a discussion of the many organelles that make up a eukaryotic cell, it is important to understand the origin of these organelles. Unlike eukaryotic cells, the prokaryotes (archaea and bacteria) lack a nucleus. It is believed that the eukaryotic cell evolved from the archaea (Mader 2008). The University of Arizona has an informative and humorous tutorial on Prokaryotes, Eukaryotes, and Viruses. I especially enjoyed this page. It is theorized that the nucleus of the eukaryotic cell was first created from a bit of the plasma membrane breaking off inside the cell and surrounding the DNA. I think of it as a process similar to endocytosis. Figure 3.3 from the text depicts how the evolution from archaea to eukaryote may have occurred. I like to think of the plasma membrane as the gate that surrounds the cell. It provides the boundary between the inside and the outside of the cell. It is the phospholipids that come together to form the bilayer that is the plasma membrane. It keeps the cell intact and is selectively permeable - that is - it only allows certain molecules and ions to enter and exit the cytoplasm freely (Mader 2008). One method by which molecules can cross the membrane freely is by diffusion, which is the movement of molecules from an area of higher concentration to an area of lower concentration. Osmosis is the term used to describe the diffusion of water across the membrane. The 'gate' can not move all the molecules by itself though. This is where the gatekeepers come in. Proteins, or the 'gatekeepers,' embedded in the plasma membrane move molecules from outside the cell to the inside or vice versa using 2 methods, facilitated transport or active transport. The carrier proteins involved in facilitated transport move molecules down their concentration gradient at a rate higher than diffusion. Because the molecules are moving down their concentration gradient, no energy is expended during facilitated diffusion. Active transport on the other hand moves molecules against their concentration gradient. This requires the expenditure of energy. Like facilitated transport, carrier proteins, now called pumps, have an affinity for a certain type of molecule. That is to say that a carrier protein binds with a specific molecule. Two additional methods that move molecules across the membrane are endocytosis and exocytosis. Both involve invagination of the plasma membrane. A pouch is formed around the molecules to be moved and eventually the pouch splits off from the membrane to form a vesicle that houses the molecules. Endocyctosis is the movement of molecules from the outside to the inside of the cell and exocytosis is the movement from the inside to the outside. Figure 3.5 from the text illustrates the fluid-mosaic model of plasma membrane structure.Just as the plasma membrane is the gate that surrounds the cell, in my mind, the nucleus is the control center. The nucleus is where the genetic code is stored in the form of DNA. Remember, it is the genetic code, or the genes, that specify the sequence of the amino acids in proteins (Mader 2008). And proteins control cell metabolism. The nucleus has its own membrane, called the nuclear envelope, separates its contents from that of the rest of the cell. The nuclear envelope is a double membrane that is continuous with the endoplasmic reticulum and contains nuclear pores that allow the passage of ribosomal subunits out of the nucleus and proteins into it (Mader 2008). Through an electron microscope, DNA is only visible in the form of chromatin, which consists of DNA and associated proteins. The nucleus also contains nucleoplasm and nucleoli. The nucleolus is the site of rRNA production and where it joins with proteins to form the subunits of ribosomes (Mader 2008). Figure 3.11 from the text shows a drawing of the nucleus with its various components along with two electron micrographs. The one to the left shows the nuclear pores and the one to the right shows both rough endoplasmic reticulum (ER) and smooth ER. Ribosomes are where protein synthesis occurs. There are ribosomes that are attached directly to the endoplasmic reticulum and others that are floating in the cytoplasm. The endoplasmic reticulum is part of the endomembrane system. The endomembrane system consists of the nuclear envelope, the ER, the Golgi apparatus, lysosomes, and vesicles. Once proteins are synthesized in the ribosomes, they enter the rough ER interior for processing and modification (Mader 2008). The smooth ER produces produces phospholipids and carbohydrates. The Golgi apparatus look like stacks of pancakes and they process, package and delivery proteins and lipids received from the ER. Lysosomes are sacs produced by the Golgi apparatus that contain digestive enzymes. Vesicles are small membranous sacs that transports substances. Figure 3.12 from the text is a great illustration of the endomembrane system. To me, the cytskeleton is the infrastructure of a cell. It provides support, it anchors things down, and it can aid in movement. The cytoskeleton is a collection of protein fibers that crisscross the cytoplasm (Mader 2008). Microtubules, actin filaments and intermediate filaments are all examples of the fibers that make up the cytoskeleton. Cilia and flagella are both made up of microtubules and aid in movement. Cilia are about 20 times shorter than flagella. Ciliated cells line our respiratory tract and a female's oviduct. Sperm cells are flagellated (Mader 2008).

Last but not least is the powerhouse of the cell. So called because mitochondria convert the chemical energy of glucose into energy the cell can use (the chemical energy of ATP molecules) (Mader 2008). This reaction is called cellular respiration. Cellular respiration includes glycolysis, the citric acid cycle and the electron transport chain. During glycolysis (anaerobic), glucose is split into two molecules of pyruvate. NADH results from hydrogen and electrons being removed from glucose. This reaction also nets 2 ATP molecules. The cytric acid cycle (aerobic) completes the breakdown of glucose and again, NADH carries away the hydrogen and electrons and 2 more molecules of ATP are produced. Carrier proteins of the electron transport chain (aerobic) accept the electrons from NADH. The net result of cell respiration is the production of 36 ATP molecules. Proteins, carbohydrates, and lipids can also be used to fuel cellular respiration. Figure 3.14from the text shows a mitochondria. The matrix contains enzymes to break down glucose and ATP production occurs at the cristae.When the body can not bring in enough oxygen to support cellular respiration, it switches to the process of fermentation to produce energy. During fermentation, glycolysis still occurs and the resulting hydrogens and electrons are still passed to NAD. When the electron transport chain is not available due to a lack of oxygen, NADH passes the hydrogens and electrons to pyruvate. The result is the production of lactate and only two molecules of ATP. Fermentation works well for bursts of energy for a short time, but as lactate builds up, muscles begin to fatigue and cramp. The energy that is produced during cell respiration or fermentation is used to power all of the processes that keep it alive. The link to the E.Coli metabolic overview map is a bit overwhelming. I am still trying to get a handle on the fact that all of those processes are happening inside of one bacteria...and that there is a protein that catalyzes each reaction. It is mind boggling.

Tissues are made up of specialized cells of the same type that perform a common function in the body (Mader 208). The first of four tissue types is the connective tissue. The main function of connective tissue is to connect and support. The three types of connective tissue, fibrous, supportive, and fluid, are all made of specialized cells, ground substance, and protein fibers. Fibrous connective tissue can be broken down further into 3 main groups: loose fibrous (protects internal organs), adipose tissue (insulates and protects kidneys and heart), and dense fibrous (tendons, ligaments). Supportive connective tissue includes the cartilages: hyaline (nose, long bones), elastic (ear), and fibrocartilage(disks in back, knee) and bone. Fluid connective tissue consists of blood and lymph. The red blood cells transport oxygen, white blood cells fight infection, and platelets form clots. Lymph is a clear watery fluid derived from tissue fluid that contains white blood cells (Mader 2008).

There are three types of muscle tissue: skeletal, smooth, and cardiac. Skeletal muscle is attached to the skeleton and causes movement in the body when it contracts. Skeletal muscle is striated. Smooth muscle is found in the walls of the viscera (intestine, bladder) and blood vessels (Mader 2008). It contracts slowly and is involuntary. Cardiac muscle is only found in the walls of the heart. Figure 4.5 illustrates and explains the three types of muscle tissue.

Nervous tissue is made up of nerve cells (neurons) and neuroglia, which support and nourish the neurons (Mader 2008). A neuron is made up of three parts. The dendrite receives signals. The cell body houses most of the cytoplasm and the nucleus. The axon conducts nerve impulses. Outside of the brain and spinal cord, fibers (neuron plus myelin) bound by connective tissue form nerves. Neuroglia outnumber neurons nine to one and take up more than half the volume of the brain (Mader 2008).

Epithelial tissue protects. It consists of tightly packed cells that form a tight continuous network. It lines body cavities and covers surfaces. The cells are anchored to a basement membrane. On the other side they are face the environment. Epithelial cells are named based on the number of cell layers and the shape of the cell (Mader 2008). There is also transitional epithelium, which changes in response to tension (urinary bladder), and glandular epithelia secretes a product (goblet cells, sweat glands) (Mader 2008). Figure 4.7 from the text shows some examples of basic epithelial tissue and where you will find each.
All of these tissues fit together in different ways to form the organs of the body. As we learned in chapter 1, our organs work together to form the organ systems. It is our organ systems working together that help us to maintain homeostasis. The nervous system processing input from the environment and along with the endocrine system, directs the rest of the organ systems. Figure 4.15 shows a great overview of what each of the major organ systems do to contribute.

REFERENCES:
Mader, Syliva S. Human Biology. New York, NY: McGraw-Hill (2008).

Links provided throughout the summary take you to online sources.


IMPORTANT NOTE: Any time "text" or "the text" is referenced in the above summary, I am referring to the textbook Human Biology by Sylvia Mader (cited directly above).