1 Foundations of Biology

work in progress!

1.1 Studying biology: the practice of science

• ^^Biology^^ - the study of living organisms
• Scientific method is used to design and perform experimental investigations.
  • Well-designed investigations take into consideration current observations and previous results.

The importance of observation

• Observations can reveal how organisms function and how they interact with others + the environment.
  • Observations take advantage of human senses and apparatus for more accurate results.
• They can be interpreted differently based on what one already knows/has experienced.

Learning by experimentation: the scientific method

• Scientists observe what is already known, then ask questions (“why?”); an experimental approach to the study of science.
• ^^Hypothesis^^- a potential justification/explanation for things that are observed.
  • Can be used to predict events/behaviour.
  • Tested in experiments to determine accuracy; the hypothesis is rejected if inaccurate, supported if accurate.
• ^^Theory^^ - if the hypothesis has been proven as correct under all the conditions that it has been tested in, it becomes this (AKA principle)

Asking the right questions: making hypotheses

• Hypotheses have to be testable, but even if it can’t be tested, it doesn’t mean it’s not correct.
• Gather information that is relevant to proving (or disproving) the hypothesis.

Choosing the right method

• Methods have to be reliable; described in sufficient detail to allow for repetitions of the experiment.
  • If similar results cannot be obtained upon repetition, it is considered unreliable.
  • Avoid personal bias; be objective when collecting and analysing data.
• Results should be clearly stated, separate from discussion of results.
• Multiple trials should be conducted, to prove that results were not because of a one-time fluke.
• Experiments and their results need to be able to replicated in order to be validated.

The need for experimental controls

• Variables that can affect experiment outcomes:
  • Time of day
  • Temperature
  • Amount of light
  • Season
  • Level of noise
• ^^Independent variable^^ - the variable that is being tested. (AKA experimental)
• ^^Dependent variable^^ - the variable that is being measured when the independent variable changes.
• ^^Controlled variable^^ - the variables that are kept constant between experiments
• ^^Control group^^ - a secondary experiment that is identical to the first, bar the single experimental variable being tested.
  • As a controlled experiment, it means that one variable at a time can be tested and its effects can be analysed.
  • Used to eliminate the effects that random factors have on results.

Making valid conclusions

• Valid conclusions depend on reliability of results and their interpretations.
• ^^Speculations^^ - suggestions on what may be occurring based on results.

^^Conclusion^^ - statement based on the observations and measurements.

\

Limitations of the scientific method

• Can only be applied to hypotheses that are testable, and to questions that can be answered.
  • e.g it is impossible to conduct experiments around ‘life after death’
• Cannot be used to test moral or ethical issues, but can predict environmental/biological impacts.

1.2 Important principles in biology

• ^^Biological principles^^ - theories that are supported by immense amounts of evidence, that make it unlikely for it to be disproved in the future.

  • Relevant to the way that almost all living organisms function.

• “Organisms are living things”

  Organisms are made of cells

  • ^^Cell theory^^ - a theory which states that all organisms are made of cells, that all cells come from pre-existing cells, and that the cell is the smallest living organisational unit.
  • All cells have a cell membrane that encloses the interior fluid, cytoplasm.
  • All cells have DNA as genetic material.

  Evolution explains diversity

  • Similarities, differences and geographic distribution of organisms → organisms have changed over time.
  • ^^Phylogeny^^ - study of evolutionary relationships between organisms.
  • ^^Scientific classification^^ - hierarchy of names based on phylogenetic relationships that encompasses all organisms.

  Characteristics of organisms

  • Common to all organisms, no matter whether plant, animal, fungi, protist or bacteria.
  • Made of cells
  • Chemically complex and highly organised
  • Exchange energy and matter in their environment
  • Sense and respond to stimuli
  • Grow and reproduce
  • Evolve

  Common requirements for life

  • All life requires a source of energy.
  • Amount of energy depends on organism type, stage of growth, activity level and reproductive state.
  • All life requires nutrients and water for growth, maintenance and repair.
  • Waste is produced as a result of the latter processes.
  • Simplicity of waste excretion depends on size of organism
  • All life is composed of water, organic compounds (proteins, carbs, lipids, vitamins) and minerals.
  • All life requires the ability to sense and respond to stimuli in their internal and external environments.

  Organisms are adapted to their environment

  • Over time, species become adapted to their external environment
  • ^^Natural selection^^ - individuals with features most suited to their environment survive and pass those features down to their offspring.
  • Inherited behaviour and functions make organisms suited for survival in their environment.

1.3 The composition of organisms

• 92 types of naturally occurring elements on Earth (NB. this is approximate and may have changed from the years this textbook was published)
• ^^Organic compounds^^ - complex compounds composed of carbon and hydrogen that are produced or found in living organisms.
• ^^Inorganic compounds^^ - all other compounds that are not formed of carbon and hydrogen.
  • They are still important for living organisms (e.g water, oxygen)

Inorganic compounds

Water

• Most organisms are 70-90% water.
• Chemical reactions that occur in cells happen in a watery medium.
• Water’s properties (such as pH and heat capacity) are very important in biological processes.
• Water molecules are cohesive; strong tendency to stick together.
• ^^Surface tension^^ - Bonds between surface of molecules.
  • Water’s surface tension allows small insects to walk across its surface without ‘breaking’ the molecule.
• ^^Heat capacity^^ - The amount of heat needed to change the temperature of an amount of matter by 1°C.
  • Water’s heat capacity is very high.
  • As chemical reactions occur in the body produce heat, water present in the body can absorb said heat without heating the cells up significantly.

Oxygen and carbon dioxide

• ^^Cellular respiration^^ - the process of releasing energy from food molecules using oxygen.
  • A constant supply of oxygen is needed to keep cells active.
  • Although oxygen can be easily obtained from the atmosphere, solely marine animals are usually small given that oxygen is not soluble in water.
  • Organisms that obtain oxygen from water are small, flat, inactive or have efficient ventilation systems (e.g gills)
• ^^Photosynthesis^^ - the process of making the organic compound glucose with a by-product of oxygen, using carbon dioxide, sunlight and water by plants.
  • Carbon dioxide is converted into energy by plants in photosynthesis, and returned to the environment through organic material decay and as a result of cellular respiration.
  • The “carbon cycle” between organisms and the atmosphere is essential to survival.

Nitrogen

• ^^Nitrogen fixation^^- the process performed by bacteria of converting atmospheric nitrogen into compounds that plants can be used.
  • Nitrogen is a key component of all proteins and thus is needed in a relatively large amount.

Minerals

• Biologically important minerals:
  • Phosphorous
  • Potassium
  • Calcium
  • Magnesium
  • Iron
  • Sodium
  • Iodine
  • Sulphur
• Mineral ions (mineral salts) are retrieved from weathered rocks and absorbed into plant roots.
  • Also found in cell cytosol, structural components such as bone, and enzyme + mineral molecules.
• Humans require more than 20 different minerals.

Organic molecules

• Four main types:
  • Carbohydrates
  • Lipids
  • Proteins
  • Nucleic acid
• Can be converted from one form to others, in places like the liver.
  • Carbohydrates are converted to fats for storage when food is plentiful.
  • The reverse occurs when food is no longer plentiful.
• Can be linked together into larger molecule chains.

Carbohydrates

• ^^Carbohydrates^^ - compounds made out of carbon, hydrogen and oxygen.
• Most abundant organic compound.
• Important source of energy for organisms.
• Plants - the carbohydrate starch is used to store energy; the carbohydrate cellulose is used to support structure.
• Animals; the carbohydrate glycogen stores energy.
• ^^Monosaccharides^^ - subunits of carbohydrates; simple sugars.
  • Glucose is an example.
  • Monosaccharides have hydrogen/oxygen in the same proportions as water, meaning two hydrogens for every oxygen.
• ^^Disaccharides^^ - two sugars joined together.
  • A molecule of water is removed.
• ^^Polysaccharides^^- many sugars joined together.

\

\

Lipids

• ^^Lipids^^ - fat and oil molecules that store energy.
  • e.g phospholipids (cell membrane component) and steroids (hormones)
• Composed of carbon, hydrogen and vitamins in different proportions to carbohydrates.
  • Smaller proportions of oxygen and can contain other elements (e.g nitrogen).

Proteins

• Thousands of differing types of proteins; functions vary widely.
• Each kind of organisms have own unique proteins.
  • e.g some are hormones, some are carrier molecules.
• All are composed of carbon, hydrogen, oxygen and nitrogen.
  • May also contain sulphur, phosphorus and other elements.
• Composed in chains of units called amino acids.
  • ^^Peptide bonds^^ - the chemical links between amino acids in proteins.
• ^^Proteomics^^- the study of all proteins in an organism.

Nucleic acids

• ^^Nucleic acids^^- genetic material of all organisms.
  • Two types: DNA (deoxyribonucleic acid) and RNA (ribonucleic acids)
  • DNA contains instructions to assemble new proteins from amino acids.
  • RNA plays a role in protein manufacture.
• Composed of subunits called nucleotides.

Vitamins

• ^^Vitamins^^ - Organic materials used by animals in small amounts.
• Used merely for normal functions.
• Can be naturally synthesised, but other vitamins must be obtained in diet (e.g humans must obtain Vitamin C in our diet because we cannot ‘create’ them ourselves)
• Vitamins can be used to make enzymes.

\