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.

Figure 1; a scientific method flowchart

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.