3.6.4.1 Principles of homeostasis and negative feedback

Homeostasis in mammals involves physiological control systems that maintain the internal environment within restricted limits. It is very important for many reasons, including:

• enzymes (e.g those involved in biochemical reactions within cells/other proteins such as channel proteins are sensitive to changes in pH and temperature). Any changes from the optimum reduce the rate of reaction and, if severe enough, may denature the enzyme and the reaction will cease altogether. Maintaining a fairly constant environment means that reactions take place at a suitable rate.
• Changes to the water potential of blood/tissue fluid may cause cells to shrink/expand as a result of water leaving/entering via osmosis. This means the cells cannot operate normally.
• The maintenance of a constant blood glucose concentration is essential to ensure a constant water potential. A constant blood glucose concentration also ensures a reliable source of glucose for respiration by cells.

Positive feedback

This occurs when a deviation from an optimum causes changes that result in an even greater deviation from the normal. As example occurs in neurones where a stimulus leads to a small influx of sodium ions (this increases the permeability of the neurone membrane to sodium ions and more ions enter).


Negative feedback
Negative feedback is when the change produced by the control system leads to a change in the stimulus detected y the receptor and turns the system off. This restores systems to their original level. 


Control of any system involves a series of stages:

• the optimum point
• a receptor
• a coordinator
• an effector
• a feedback mechanism

The possession of separate mechanisms involving negative feedback controls departures in different directions from the original state, giving a greater degree of homeostatic control as the return to the optimum can be brought about faster.

For example, if there is a fall in blood glucose concentration this is detected by receptors on the cell-surface membrane of alpha cells in the pancreas. These secrete glucagon which causes liver cells to convert glycogen to glucose to raise the blood glucose concentration. There is now reduced stimulus so the secretion of glucagon reduces.

If blood glucose concentration rises insulin will be produced from beta cells in the pancreas. Insulin increases the uptake of glucose by cells (it is converted to glycogen and fat). There is now reduced stimulus so the production of insulin reduces.

3.1.4.2 Many proteins are enzymes

Enzymes are globular proteins that act as catalysts by altering the rate of a chemical reaction without undergoing permanent changes themselves. They can be reused and are therefore effective in small amounts. They catalyse a wide range of intracellular and extracellular reactions that determine structures and functions from cellular to whole-organism level.

The minimum amount of energy required to activate the reaction is known as the activation energy. For reactions to occur initially (naturally) a number of conditions must be satisfied:

• The substrates must collide with sufficient energy to alter the arrangement of their atoms to form the produce
• The free energy of the products must be less than that of the substrates

The activation energy must be initially overcome before the reaction can proceed. Enzymes lower the activation energy level. A specific region of the enzyme (the active site) is functional. It forms a small depression within the much larger enzyme molecule. Enzymes act upon substrates which fit neatly into the active site forming an enzyme-substrate complex. The substrate is temporarily held in place by temporary bonds between amino acids of the active site and groups on the substrate.

We need to know a bit about the induced fit model of an enzyme. The induced fit model proposes that the active site forms as the enzyme and substrate interact. The proximity of the substrate leads to a change in the enzyme that forms the functional active site. As it changes shape the enzyme puts strain on the substrate molecule. This strain distorts particular bonds in the substrate and consequently lowers the activation energy needed to break the bond.

We need to know about the effects of certain factors on the rate of enzyme controlled reactions. Providing there are no limiting factors the following will occur:

• enzyme concentration
• the more enzymes the more active sites so the faster the reaction
• substrate concentration
• the more substrates the faster the reaction
• concentration of competitive and non-competitive inhibitors
• competitive inhibitors block the active site. The more competitive inhibitors the lower the rate of reaction
• non-competitive inhibitors distort the active site. The more non-competitive inhibitors the lower the rate of reaction
• pH
• A pH far from the enzymes optimum will denature the enzyme and the reaction will cease
• at optimum pH the rate of reaction will be the fastest
• temperature
• A temperature far from the enzymes optimum will denature the enzyme and the reaction will cease
• at optimum temperature the rate of reaction will be the fastest

Okay so we need to be able to calculate pH from hydrogen ion concentration. To do this we use the equation:

pH = - log [H+]

3.1.5.1 Structure of DNA and RNA

Okay so we need to know alllll about DNA and RNA. To start, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) are important information-carrying molecules. In all living cells, DNA holds genetic information and RNA transfers genetic information from DNA to the ribosomes. Ribosomes are formed from RNA and proteins. Both DNA and RNA are polymers of nucleotides. Each nucleotide is formed from a pentose, a nitrogen-containing organic base and a phosphate group. That was a nice little summary.


The components of a DNA nucleotide are:

•  deoxyribose
• a phosphate group
• one of the organic bases:
•  adenine
• cytosine
• guanine
• thymine

The components of an RNA nucleotide are:

• ribose
• a phosphate group
• one of the organic bases:
• adenine
• cytosine
• guanine
• uracil

A condensation reaction between two nucleotides forms a phosphodiester bond. A DNA molecule is a double helix with two polynucleotide chains held together by hydrogen bonds between specific complementary base pairs. In DNA, adenine binds to thymine and guanine binds to cytosine. It follows that a DNA molecule will have the same percentage of adenine/thymine, and the same percentage of cytosine/guanine.

An RNA molecule is a relatively short polynucleotide chain. It is also single stranded.

3.4.7 Investigating diversity

Genetic diversity within, or between species, can be made by comparing:

• the frequency of measurable or observable characteristics
• this is based on he fact that each observable characteristic is determined by a gene/genes
• it has limitations because a large number of them are coded for by more than one gene (they are polygenic) so they are not discrete but actually vary continuously. It is therefore often difficult to distinguish one from another.
• the base sequence of DNA 
• we can do this because of DNA sequencing
• we can measure the genetic diversity of a species by sampling the DNA of its members and sequencing it to produce a pattern of coloured bands (as each base is tagged with a fluorescent dye). Analysis of these patterns allows us to compare one species with another/the individuals of the same species.
• the base sequence of mRNA
• mRNA is coded for by DNA
• it follows that, since we can measure genetic diversity with DNA, we can measure it with mRNA.
• the amino acid sequence of the proteins encoded by DNA and mRNA
• the amino acid sequence is coded for by mRNA which is coded for by DNA.
• Genetic diversity can therefore be measured by comparing the amino acid sequences of organisms proteins.

Quantitative investigations of variation

Random sampling
There are several reasons why measurements might not be representative of the population. These include:

• sampling bias
• the selection process may be biased
• chance
• individuals by pure chance may not be representative

The best way to prevent sampling bias is to eliminate any human involvement in choosing the samples. This can be achieved by random sampling. For example:

• divide the area into a grid (e.g stretch two tape measures perpendicular to each other)
• use a random number generator to obtain a series of coordinates
• take samples at the intersection of the coordinates

We can minimise chance by:

• using a large sample size
• analysing the data collected using statistical tests

It is important to understand that gene technology has caused a change in the methods of investigating diversity. E.g DNA differences from measurable/observable characteristics has been replaced by direct investigation of DNA sequences.

3.4.6 Biodiversity within a community

Okay so first it's probably a good idea for us to learn some terms:

• species diversity is the number of different species and the number of individuals of each species within any one community
• genetic diversity is the variety of genes possessed by the individuals that make up a population of a species
• ecosystem diversity refers to the range of different habitats from a small local habitat to the whole of the Earth

A good measurement of species diversity (the number of different species and the number of individuals of each species within any one community) is species richness. Species richness is a measure of the number of different species in a community. One way of measuring species diversity is to use the equation:

d = (N(N-1))/(Σn(n-1))

NOTE:
d = index of diversity
N = total number of organisms of all species
n = total number of organisms of each species

An index of diversity describes the relationship between the number of species in a community and the number of individuals in each species.


Efforts to provide enough food for the human population at a low cost has led to a reduction in biodiversity. This is because basically as natural ecosystems develop they become complex communities with a high index of diversity. However, agricultural ecosystems are controlled by humans and farmers often select species for particular qualities to make the farms more productive. Any particular area can only support a certain biomass. If most of the area is taken up by the desirable species there is smaller area for the other species and the other species must out-compete one another for the small area. Furthermore, pesticides exclude species that compete for light/mineral ions/water/food required by the farmed species.

We need to know about the balance between conservation and farming. Certain practices that have (directly) reduced species diversity include:

• removing hedgerows
• creating monocultures
• draining marshland/filling in ponds
• over-grazing of land

Practices that have indirectly reduced species diversity include:

• the use of pesticides/inorganic fertilisers
• escape of effluent from silage stores/slurry tanks into water courses
• absence of crop rotation

A number of management techniques can be applied to increase species diversity without largely raising food costs/lowering yields. These include:

• maintaining hedgerows
• planting hedges as boundaries instead of fences
• maintaining ponds
• planting native trees
• using organic fertilisers
• reducing the use of pesticides
• using crop rotation that includes a nitrogen-fixing crop
• creating natural meadows

3.1.5.2 DNA replication

The semi-conservative replication of DNA ensures genetic continuity between generations of cells. It takes place as follows:

• The enzyme DNA helicase breaks the hydrogen bonds between the complementary base pairs of DNA
• The double helix separates into two strands and unwinds (as a result)
• Each exposed polynucleotide strand acts as a template to which complementary free nucleotides bind by specific base pairing
• Nucleotides are joined together by DNA polymerase which forms the sugar-phosphate backbone in a condensation reaction
• Each DNA molecule contains one new and one original strand, hence the name semi-conservative.

Watson and Crick devised this model of DNA replication. If i'm very honest, i'm not sure what the spec means by we need to be able to evaluate the work of scientists in validating this experiment(?). Please help if you know:)

3.4.5 Species and taxonomy

Okay so we sorta need to know a bit about how organisms are classified and named etc (naming system isnt rly important but it sort of is good to know so i'll put it in, just skip to the next paragraph if you cba to read it)...

We use the binomial naming system. The first name is the generic name (this is the name of the genus, think GENeric=GENus). Next is the specific name (this is the name of the species, think SPECIfic=SPECIes). For example, Homo sapiens (us). This tells us that we belong to the homo genus and sapiens species.

A species is a set of organisms that are able to breed to produce fertile offspring.


Courtship behaviour
Individuals can recognise members of their own species by the way they act (the behaviour of members of the same species is more similar than that of different species). Reproduction is necessary for a species to survive (duh). It is important that mating is successful as it will lead to maximum chance of species survival. Courtship behaviour enables individuals to:

• recognise members of their own species
• identify a mate that is capable of breeding (e.g is sexually mature)
• form a pair bond
• synchronise mating
• become able to breed

Courtship behavior is often used by males to determine which females are at the receptive stage (in most species, females only produce eggs for a short amount of time). 

Classification

The grouping of organisms allows better communication between scientists and avoids confusion. Classification is the grouping or organisms. there are two main types of classification:

• Artificial classification
• this divides organisms according to things that are useful at the time (e.g colour, size, etc). These features are described as analogous characteristics where they have the same function but not he same evolutionary origins (e.g butterfly and bird wings originated differently but are both used for flight).
• Phylogenic classification
• this is based upon evolutionary relationships between organisms and their ancestors. it arranges the groups into a hierarchy in which the groups are contained within larger groups with no overlap.
• it attempts to arrange species into groups based on their evolutionary origins and relationships
• Each group is called a taxon (plural taxa)
• one hierarchy comprises the taxa:
• domain
• kingdom
• phylum
• class
• order
• family
• genus
• species. 

NOTE: The theory and practice of biological classification is taxonomy.