MIT Hierarchical Introductory Biology Concept Framework

1. Biology is based on observational and experimental science.

1-1. We think what we think because we can draw conclusions from the results of controlled experiments.

1-2. An informative experiment is designed to distinguish between hypotheses.

1-3. All experiments must have controls to be informative and interpretable.

1-4. Models based on experimental data should have predictive powers.

1-5. There are often exceptions

 

2. At the molecular level, biology is based on three-dimensional interactions of complementary surfaces.

2-1. All molecules are 3D objects (2D is just a representation).

2-2. Structure of a molecule enables its function.

2-3. Interaction between molecules happens by shape matching/fitting with the use of chemical entities in the faces of the interacting molecules.

2-4. Altering the specificity of interactions is possible with minor structural modifications.

2-5. All interactions in a cell happen because of a combination of molecular forces.

2-6. Many of the physical properties of water are due to hydrogen bonds

3. The cell is the basic unit of life.

3-1. A cell has all of the machinery necessary to perform metabolism and reproduction.

3-2. A cell is separated by a membrane from the environment (compartmentalized).

3-3. A virus is not alive because it requires a host cell to perform metabolic functions.

3-4. No cell lives in the absence of other cells; cells communicate with and often depend on each other. See 5.

3-5. There are two major categories of cells: those with a nucleus (eukaryotes) and those without a nucleus (prokaryotes).

3-6. There are three major categories of organisms: bacteria, archaea, and eukaryotes. See 4-6.

4. All cells share many processes/mechanisms.

4-1. Many metabolic pathways are conserved across evolutionary spectrum (e.g. glycolysis).

4-2. The same genetic code is used by both prokaryotes and eukaryotes. See 3-5, 7-1.

4-3. All organisms use ATP as their primary energy currency.

4-4. Many aspects of eukaryotic cell structure and function have remained unchanged or minimally modified throughout evolution. See 3-5, 4-5.

4-5. Basic research on microorganisms is relevant to understanding human cellular biology and human disease.

4.6 There are three major categories of cells: bacteria, archaea, and eukaryotes. Some processes are shared between the groups and some are not. See 3-6.

5. Cells interact with other cells.

5-1. Each cell communicates with other cells that are either near or far away.

5-2. Cells communicate by releasing physical objects—i.e.molecules— or by binding each other directly. See 2-2, 2-3, 12-3.

5-3. Groups of cells work together to make tissues and organs. See 18.

5-4. Communities of unicellular organisms share information.

5-5. Organisms communicate information to each other about their environment. See 17.

5-6. Sexually reproducing organisms require other organisms to have offspring. See 6-3, 10-1.

6. Cells are created from other cells.

6-1. Cells formation by spontaneous generation has never been observed.

6-2. As a result of cell division, one cell becomes two.

6-3. In sexual reproduction, two gametes join to form a zygote. See 5-6, 10-1.

6-4. One cell division can give rise to two cells that will differentiate into two distinct cell types, serving two distinct functions.

7. DNA is the source of heritable information in a cell.

7-1. The amino acid sequence of proteins is encoded in DNA. See 8-1, 8-2.

7-2. Information is encoded in DNA, using different languages that are recognized by different machinery.

7-3. When DNA is mutated, the information it contains may be changed.

7-4./8-1-2. Segments of DNA that contain all of the information to encode the sequence of a product and regulate its expression are called genes.

8. A gene is the functional unit of heredity.

8-1. A gene is composed of DNA and

8-2. Which genes are expressed at a given time is determined by the integration of internal and environmental signals received by a cell.

8-3. Factors determining traits (genes) are inherited as discrete entities.

8-4. An allele is a particular version of a gene.

8-5. A phenotype is a trait, a genotype is the set of alleles conferring that trait.

8-6. Dominant and recessive refer to phenotypes not genotypes.

8-7. Chromosomes are made up of a set of physically linked genes.

8-8. By identifying the gene that differs from wildtype in a mutant displaying a phenotype of interest we can determine which gene is responsible for that phenotype.

8-9. Inheritance modes in humans fall into 6 major categories

8-10. The pattern of affected individuals can help determine the mode of inheritance of a phenotype. Things to consider are:

8-11. Genes can be transferred not only from parent to offspring (vertically), but also from one individual to another (horizontally).

9. The structure of DNA dictates the mechanism of the production of nucleic acids and proteins.

9-1. DNA is usually double-stranded.

9-2. Nucleic acids are polymerized in only one direction (5’ to 3’).

9-3. In vivo proteins are polymerized from the amino terminus to the carboxyl terminus (N to C).

 

10. Sexual reproduction is a powerful source of variation.

10-1. Sexually reproducing diploid organisms get one copy (allele) of each gene from each parent and pass one allele on to each of their offspring at random. See 8-3.

10-2. Diversity is introduced in gamete formation.

 

11. Life processes are the result of regulated chemical reactions.

11-1. Life obeys all of the laws of chemistry and physics.

11-2. All cellular processes consist of changes in chemical interactions

11-3. All biological macromolecules are created by chemical reactions involving monomers.

11-4. ∆G⁰ is a thermodynamic property—an inherent characteristic of a reaction regardless of starting conditions.

11-5. Life could not exist without enzymes to speed up reactions.

11-6. All cells use the same common currencies to drive energetically unfavorable reactions.

 

12. Proteins perform many varied functions in a cell.

12-1. Proteins can be enzymes that catalyze reactions. See 11-5.

12-2. Proteins can interact with each other and nucleic acids to regulate the production of proteins and nucleic acids.

12-3. Proteins can detect and transmit signals from the outside of the cell. See 5-2.

12-4. Proteins can provide structure and shape to a cell or part of a cell.

12-5. Proteins can transport things around in a cell.

12-6. Other molecules (nucleic acids, sugars, lipids, small ligands) all interact with proteins to accomplish their functions (including the functions listed above). See 7-2.

12-7. Cells make thousands of different proteins simultaneously.

 

13. Recombinant DNA technology allows scientists to manipulate the genetic composition of a cell.

13-1. Recombinant DNA is a set of tools that allows scientists to move between genetics, biochemistry and molecular biology – allowing us to determine how the parts of a cell or organism work.

13-2. Many of the techniques and reagents used in recombinant DNA technology are adaptations of processes that exist in nature.

13-3. Recombinant DNA techniques can be used to help identify the gene responsible for a trait.

13-4. PCR allows the exponential amplification of a particular DNA sequence.

13-5. Homologous recombination can be used to introduce a modified gene into an organism

 

14. The expression of genes is regulated.

14-1. Not all genes need to be expressed at all times.

14-2. RNA Polymerase and regulator proteins (trans-acting elements) interact with regulatory regions (cis-acting elements) by binding to either promote or prevent transcription. See 2.

14-3. Components of processes that work together are often regulated together.

 

15. All carbon-containing biomass is created from CO₂.

15-1. All organisms utilize organic nutrients, in particular organic carbon, to live and grow—accumulate biomass.

15-2. Someorganisms are able to convert inorganic carbon in CO₂ into organic carbon through photosynthesis.

15-3. Aerobic respiration consumes O₂ and releases CO₂ into the atmosphere.

15-4. Photosynthesis consumes CO₂ and releases O₂ into the atmosphere.

15-5. If Photosynthesis = Respiration, the global carbon cycle is in equilibrium and no changes to the environment are introduced.

 

16. Populations of organisms evolve because of variation and selection.

16-1. Mutation, recombination, and exual reproduction are genetic sources of variation.

16-2. Mutations can result in a change in phenotype.

16-3. Selection occurs on the level of the individual.

16-4. Thousands of genes are passed from parents to offspring, almost all without new mutations.

16-5. Evolution proceeds without a goal, it is a random process. See 17.

 

17. Organisms and the environment modify each other.

17-1. The environment places selective pressure on organisms—selection favors "mutants" that are better able to survive in the environment.

17-2. The products of organisms’ life cycle return to the environment, modifying it.

 

18. In multicellular organisms, multiple cell types can work together to form tissues which work together to form organs.

18-1. The immune system protects a host from foreign invaders.

18-2. Development of a multicellular organism from a single cell occurs stepwise. See 6.

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