CHAPTER 6
Biology
Biology is likely to be a required module on the A2 test you take. The test covers just the basics of biology, so if you have taken college-level courses, you will be a step ahead.
SCIENTIFIC METHOD
The scientific method is a process for scientific exploration and experimentation. Typically, it begins with observations and the formulation of questions. The process might look like Figure 6.1.
Figure 6.1 The Scientific Method
In the testing, or experimental, phase of the process, scientists look for causal relationships. They determine variables that will help them to answer their question.
• Independent variable: This is what changes to answer the question. If the question is “What kind of plant food helps plants grow taller?,” the independent variable is the kinds of plant food.
• Dependent variable: This is what responds to the independent variable. For the question above, the dependent variable is the height of the plants.
• Constant: These remain the same in all cases so that you can see the true causal relationship of the independent variable on the dependent variable. Constants for the question above might include type of soil, amount of light, and amount of water.
• Controlled variable: This is the standard of comparison in an experiment. If your question were, “What kind of plant food helps plants grow taller?,” your control might include a plant that was not given any plant food at all.
Two kinds of reasoning may apply to a given experiment. When a scientist formulates a hypothesis and then tests it, moving from a general statement to specific observations, that process is called deductive reasoning. When a scientist starts with specific observations and creates a generalization or theory to explain them, that process is called inductive reasoning.
An experiment is reliable if it is consistent and repeatable. If one scientist repeats the experiment many times with similar results, the test is reliable. If many different scientists perform the same experiment and achieve the same results, the test is reliable.
An experiment is valid if it measures what it is supposed to measure. If controls and constants are maintained, methodology is sound, instruments are appropriately sensitive, and the results may be applied or generalized beyond the single study, the test may be valid. The more measurements that are made, and the greater the size of the subject population, the more valid an experiment is likely to be.
Test Yourself
1. Once a scientist develops a question about observations, he or she formulates a __________.
2. What kind of reasoning does Figure 6.2 illustrate? __________
Figure 6.2 One Form of Reasoning
3. A vet student is testing the question: “Which brand of dog food best promotes a shiny coat?” What might be a reasonable constant?
A. Dog breed
B. Brand of food
C. Warmth of room
D. Dryness of food
Answers
1. hypothesis. Look back at the graphic to see the order of the process.
2. inductive. Deductive reasoning would start with a theory.
3. A. The student would not want to compare coats across breeds because the variations might mask the causal relationship being tested.
TAXONOMY
In biology, taxonomy is the branch of science that classifies organisms. Figure 6.3 shows the classification strata from most general at the bottom to most specific at the top.
Figure 6.3 Classification Levels
For example, imagine a common house mouse. In order, from domain to species, the house mouse is classified Eukarya, Animalia, Chordata, Mammalia, Rodentia, Muridae, Mus, musculus. Its common Latin name, also known as its binomial name, is simply Mus musculus.
Scientists compare species in a variety of ways. They may look at their structures. Vertebrates, for example, have closed transport, or closed circulatory systems, with blood carried within vessels and pumped by a heart. Certain invertebrates, such as mollusks and arthropods, have open transport, or open circulatory systems, with a heart that pumps blood into open body cavities.
There are a number of other ways to classify living organisms. For example, the energy pyramid looks at whether organisms are producers (acquiring energy from the sun and not feeding on other organisms) or consumers (acquiring energy from other organisms). Consumers are further divided, as in Figure 6.4.
Figure 6.4 Energy Pyramid
Within the plant kingdom, plants are often divided into spore-producing plants such as mosses and ferns, and seed-producing plants. Seed-producing plants are further divided into gymnosperms (with naked seeds, such as pine trees) and angiosperms (flowering plants with enclosed seeds, such as apple trees).
MOLECULES
A molecule is a bonded group of atoms. Two or more like or unlike atoms may bind together to form a molecule. If the atoms are unlike, the molecule is called a compound. O2 is a molecule, and so is H2O. But only the latter is a compound.
Molecules may be polar, with positive charges grouped on one side and negative charges on the other. H2O is one such molecule. Molecules may be nonpolar, with electrons distributed more symmetrically. CO2 is nonpolar. Polar and nonpolar molecules do not mix well together to form solutions.
Organic compounds are the ingredients that make up living organisms. All organic compounds contain a carbon atom. There are four classes of organic compounds: carbohydrates, lipids, proteins, and nucleic acids.
Carbohydrates
Carbohydrate compounds contain only carbon, hydrogen, and oxygen. Typically, there are two hydrogen atoms and one oxygen atom for each carbon atom in a carbohydrate compound. (See Table 6.1.)
Table 6.1 Types of Carbohydrates
Lipids
Lipids, like carbohydrates, are primarily carbon, hydrogen, and oxygen, but they have much less oxygen than carbohydrates do and are insoluble in water. (See Table 6.2.)
Table 6.2 Types of Lipids
Proteins
Proteins are made up of carbon, hydrogen, oxygen, and nitrogen, bonded to form compounds called amino acids. Like all organic acids, they contain the COOH group, but in addition, they have an amino group, NH2. Both bond to the same carbon atom in the compound.
Condensation reactions between the COOH groups and the NH2 groups bond amino acids together to form chains. The bonds are known as peptide bonds, and the chains are polypeptide chains. The chains coil and fold in different patterns, and these patterns suggest one way to classify proteins. (See Table 6.3.)
Table 6.3 Types of Proteins
Nucleic Acids
These building blocks of genetic material are made up of carbon, hydrogen, oxygen, nitrogen, and phosphorus. More specifically, each nucleotide that comprises nucleic acid contains a (CH2O)5 (pentose) sugar, one or more phosphate groups, and one of five nitrogenous bases. In RNA, the sugar is ribose. In DNA, the sugar is deoxyribose. The possible bases are adenine, cytosine, guanine, thymine, and uracil.
More about nucleic acids appears later in this chapter.
CELLS
A cell is the smallest structural and functional unit of an organism. With the exception of viruses, all living organisms are composed of cells. Cells range in size from the tiniest of bacteria to the relatively enormous egg of an ostrich.
Parts of a Cell
All cells contain a cell membrane, cytoplasm, and DNA. Cells may be prokaryotic, in which case they lack a nucleus or other internal, walled-off structures. They may be eukaryotic, housing a nucleus and other organelles.
Bacteria are one domain of prokaryotic cells. They come in four basic shapes—spherical (cocci), rod-shaped (bacilli), spiral-shaped (spirochete), and comma-shaped (vibrio). No matter the shape, all contain the same basic structures.
Animal cells differ from plant cells in certain structures. Figure 6.5 illustrates parts of an animal cell.
Figure 6.5 Animal Cell
• Centriole: Made of microtubules, this small organelle aids in cell division.
• Cytoplasm: This fluid fills the cell, provides its shape, and contains molecules that break down waste and aid in metabolism.
• Golgi body: This organelle stores, sorts, processes, and releases products from the endoplasmic reticulum.
• Lysosome: This digests excess materials from the cytoplasm, using a variety of enzymes to break down molecules.
• Microtubule: This structure aids with transport and motility, including movement of chromosomes during mitosis.
• Mitochondrion: Through cellular respiration, this organelle breaks down nutrients to produce energy.
• Nucleus: This organelle stores the cell’s genetic material and coordinates cellular activity from protein synthesis to reproduction.
• Nucleolus: A small structure in the nucleus, this body makes ribosomal RNA (rRNA), a key element in the construction of proteins.
• Nucleopore: The nuclear membrane is strong and protective, but these small holes help to channel nucleic acids and proteins in and out as needed.
• Ribosome: This mix of RNA and proteins is the site of protein synthesis and may float free or attach to the endoplasmic reticulum.
• Rough endoplasmic reticulum: This network of tubes is dotted with ribosomes and aids in protein production and transport.
• Smooth endoplasmic reticulum: Lacking ribosomes, this smooth network of tubes helps to produce and metabolize fats and steroid hormones.
Plant cells have a few parts that animal cells lack. On the other hand, they do not have lysosomes, and most plant cells lack centrioles as well. (See Figure 6.6.)
Figure 6.6 Plant Cell
• Cell wall: This layer of polysaccharides supports and protects the cell. It is found in most prokaryotes as well as in fungi and plants.
• Chloroplast: This is one of several plastids, or small organelles, in plant cells only. It contains chlorophyll and is the site of photosynthesis.
• Filamentous cytoskeleton: This protein structure gives the cell shape and aids in movement and transport. It exists in animal cells as well.
• Peroxisome: This organelle helps with a number of metabolic functions. It exists in animal cells as well.
• Plasma membrane: This layer of lipids and proteins forms the boundary of a cell or vacuole and regulates movement of molecules in and out of the cytoplasm. It exists in animal cells as well.
• Plasmodesmata: This narrow filament of cytoplasm connects plant cells and allows for transport and communication.
• Vacuole: This large organelle contains and stores water, enzymes, and waste products. It is found in all plant and fungal cells as well as in some animal and prokaryote cells.
Transport
Molecules of water, oxygen, and nutrients are always moving into a cell, and waste products are always moving out.
When molecules move from areas of high concentration to areas of low concentration, no energy is required. That movement is called passive transport. (See Table 6.4.)
Table 6.4 Types of Passive Transport
When molecules move from areas of low concentration to areas of high concentration, chemical energy is required, usually from the high-energy molecule known as ATP (adenosine triphosphate). That movement is called active transport. (See Table 6.5.)
Table 6.5 Types of Active Transport
Tonicity
Tonicity is the relationship between the concentrations of solutes on either side of a membrane. A cell may have one of three different relationships to its surroundings:
• Isotonic: The concentration of solutes is the same; there is no net movement of water between the cell and its environment.
• Hypertonic: The concentration outside the cell is greater than inside the cell; water leaves the cell via osmosis, and the cell shrinks.
• Hypotonic: The concentration inside the cell is greater than outside the cell; water moves into the cell via osmosis, and the cell swells or bursts. (See Figure 6.7.)
Figure 6.7 Solutions
CELLULAR RESPIRATION
Cells derive energy via cellular respiration, which breaks down glucose.
C6H12O6 + 6O2 → 6CO2 + 6H2O + energy
In this formula, glucose plus oxygen yields carbon dioxide, water, and energy in the form of heat and ATPs. The process has three main steps, with most of the action taking place in the mitochondria of the cell.
1. The first step in cellular respiration is the breaking down of glucose, or glycolysis. In an anaerobic process, carbon in glucose breaks into two three-carbon strands called pyruvates. The net gain of ATPs in this step is 2 ATPs. A small amount of NADH (nicotinamide adenine dinucleotide) is also made.
2. The second step in cellular respiration is the Krebs cycle (or citric acid cycle), which is aerobic—it requires oxygen. The net gain of ATPs in this step is 2 ATPs. NADH and FADH2 (flavin adenine dinucleotide) are byproducts of this step.
3. The final step in cellular respiration is the electron transport chain, which is also aerobic. Hydrogen electrons are transported via NADH down a chain. This step produces most of the ATPs in cellular respiration—as many as 34 in all.
If no oxygen exists, the byproducts of glycolysis may instead go through the process of fermentation, producing either alcohol or lactic acid and releasing carbon dioxide.
PHOTOSYNTHESIS
Plants and some bacteria and protists use the process of photosynthesis to convert light energy into chemical energy that can provide fuel for the organism’s growth, movement, and other metabolic work.
6CO2 + 6H2O + photons → C6H12O6 + 6O2
In this formula, six molecules of water combine with six molecules of carbon dioxide, and with the assistance of light, they produce one molecule of sugar plus six molecules of oxygen. The process has two steps:
1. In light-dependent reactions, energy from the sun is absorbed by chlorophyll and converted to energy in the form of ATP and NADPH (which is a reduced form of NADH).
2. In light-independent reactions, also known as the Calvin cycle, energy from ATP and NADPH fixes (converts inorganic molecules to organic compounds) CO2 to form carbohydrates.
In plants, this process takes place in the chloroplasts in the leaves. (See Figure 6.8.)
Figure 6.8 Cross-Section of a Leaf
In flowering plants, photosynthesis is a key factor in providing the energy to reproduce. The stamen contains the male pollen in its anther. Pollen lands on the stigma and proceeds down the style to the ovary. (See Figure 6.9.)
Figure 6.9 Parts of a Flowering Plant
CELLULAR REPRODUCTION
Cellular reproduction allows a parent cell to pass on genetic information to daughter cells through a process of cell division.
Binary Fission
Prokaryotes, such as bacteria, reproduce using binary fission. The cell replicates its genetic material, grows larger, and then divides into two similarly-sized daughter cells through the process called cytokinesis.
Mitosis
Like binary fission, mitosis is a form of asexual reproduction, in that it produces daughter cells that are genetically identical to the parent cell. Mitosis is preceded by interphase, during which the cell grows, duplicates its chromosomes, and grows some more. (See Figure 6.10.)
Figure 6.10 Phases of Mitosis
1. Prophase: The duplicated chromosomes condense, the nuclear membrane breaks down, and a spindle apparatus forms at each end (pole) of the cell.
2. Metaphase: Condensed chromosomes line up and attach to the spindle.
3. Anaphase: Chromosomes separate into sister chromatids, which migrate toward opposite ends of the spindle.
4. Telophase: The spindle breaks down, and nuclear membranes form around each new set of chromosomes, preparing for cytokinesis, which results in daughter cells.
Meiosis
Whereas mitosis generates cells used for growth or regeneration, meiosis is the form of cellular division that generates cells used for sexual reproduction, the cells called gametes. Mitosis produces two diploid daughter cells that are copies of the parent cell. Meiosis produces four haploid cells—each contains half the chromosomes of the parent cell. (See Figure 6.11.)
Figure 6.11 Phases of Meiosis
The process begins with meiosis I.
1. Prophase I: The duplicated chromosomes condense, and pair up, aligning with their partners and forming tetrads of four chromatids each. Homologous chromosomes may trade (recombine) parts in the process called crossing over. The nuclear membrane breaks down.
2. Metaphase I: Tetrads align, with centromeres of homologous chromosomes facing opposite ends of the cell.
3. Anaphase I: Chromosomes migrate to opposite ends of the cell, with sister chromatids remaining together.
4. Telophase I: Each end of the cell ends up with a haploid number of sister chromatids that are not identical. Nuclear membranes re-form around the new sets of chromosomes in preparation for cytokinesis.
The process may continue with meiosis II, which bears many similarities to mitosis.
1. Prophase II: Chromosomes condense, the nuclear membrane breaks down, and a spindle apparatus forms at each pole of the haploid cell.
2. Metaphase II: Condensed chromosomes line up and attach to the spindle.
3. Anaphase II: Chromosomes separate into sister chromatids, which migrate toward opposite ends of the spindle.
4. Telophase II: The spindle breaks down, and nuclear membranes form around each new set of chromosomes, preparing for cytokinesis, which results in daughter cells.
The end result of meiosis I and II, then, is the production of four daughter cells containing one chromatid apiece. In human reproduction, these might be four sperm cells, or they might be one functional egg cell and polar bodies, cells that do not develop into ova. Some invertebrates and occasionally some snakes or fish may reproduce via parthenogenesis, in which the animal clones itself using a polar body and bypasses fertilization entirely.
GENETICS
Genetics is the study of heredity, the inheritance of traits from a parent. The science began with observations of physical traits of plants by an Austrian monk, Gregor Mendel. Mendel’s plant-breeding experiments led him to posit the existence of invisible factors that caused certain traits to be dominant or recessive. By the 1900s the invisible factors were called genes, but it would take some time before scientists understood how they worked.
Punnett Squares
An English geneticist, Reginald Punnett, devised a visual way to map and predict inheritance of physical traits, or phenotypes. A phenotype is a combination of alleles, forms of genes that are inherited from parents. It may be expressed as a genotype, a description of the dominant and recessive traits inherited.
This Punnett square shows the connection of genotype to phenotype. Here, the dominant trait is purple flowers. The recessive trait is white flowers. (See Figure 6.12.)
Figure 6.12 Punnett Square
In the square, male pollen from a flower with heterozygous (having one each of two alleles) traits for purple flowers (Pp) pollinates the pistil of another flower with heterozygous traits for purple flowers (Pp). The resulting offspring have one of three possible genotypes. One (1/4 of the square) is homozygous (having two of the same allele) dominant for purple flowers (PP). One (1/4 of the square) is homozygous recessive for white flowers (pp). Two (1/2 of the square) are heterozygous dominant for purple flowers (Pp). So in any four offspring, you would predict that three will have purple flowers and one will have white flowers. An offspring with purple flowers may have the homozygous dominant genotype (PP) or the heterozygous genotype (Pp). There is no way to tell without doing more experimenting.
Sometimes, a recessive gene represents a certain disease that is only expressed when the offspring’s genotype is homozygous recessive; for example, dd. If the offspring’s genotype is heterozygous, Dd, we say that the offspring is a carrier of that disease. The disease may not be expressed, but it may be passed down, or inherited.
A sex-linked trait is one that is carried only by a male or a female parent. In humans, men usually have XY chromosomes, whereas women have XX. Only men, then, can inherit Y-linked traits, but either men or women may inherit X-linked traits.
DNA
Although scientists recognized that a molecule of inheritance existed, it took decades of experimentation in the early to mid-twentieth century to determine just what that molecule was and how it worked. The components of the molecule were isolated by Phoebus Levene in 1929:
• Adenine (A)
• Cytosine (C)
• Guanine (G)
• Thymine (T)
• Sugar (deoxyribose)
Levene determined that the DNA molecule was composed of a series of nucleotides linked together in the following order: phosphate-sugar-base. Not until the Rosalind Franklin–inspired James Watson and Francis Crick model in 1953 did scientists understand precisely how those pieces fit together. (See Figure 6.13.)
Figure 6.13 DNA Replication
The Rosalind Franklin–inspired Watson-Crick model envisions DNA as a spiraling helix, or ladder, with bases aligning to form the steps. Adenine pairs with thymine, and cytosine pairs with guanine. When DNA replicates, the helix unwinds, and some of the steps split apart. Enzymes called DNA polymerases bind along the single strands, read the nucleotides, and find and position complementary nucleotides until a complete copy is formed.
The genetic code in DNA tells the cell how to build a protein. DNA never leaves the nucleus of a cell. Instead, it locates and copies the gene to make the given protein into a messenger called mRNA. This messenger RNA can travel out of the nucleus to the ribosomes where proteins are made. This process of copying is called transcription.
Unlike DNA, RNA is single-stranded, and its sugar is ribose instead of dioxyribose. In the process of transcription, all thymine bases in DNA change to uracil bases in RNA.
The ribosome reads the mRNA message three nucleotides at a time (in groups called codons) and uses transfer RNA (tRNA) to locate appropriate amino acids based on those codons. The finished chain of amino acids is the protein. This process of reading and constructing is called translation.