AS Biology Unit 2

Studying large large quantities is not practical, so biologists take samples. Sampling is taking measurements of individuals selected from the population of the organisms being studied. This is supposed to be representative but they are sometimes not, including: 
Sampling bias. The selection process may be biased. The investigators may be making unrepresentative choices, on purpose or by accident.
Chance. Even if bias is avoided, the individuals chosen by by chance not be representative. 
Random sampling is used to avoid this. Use a large sample size and analyse the collected data at the end. 

Causes of variation arise from:
Mutations  - sudden changes to genes and chromosomes. 
Meiosis - this nuclear division forms gametes and mixes up the genetic material, all of which are different, before it is passed into the gamete.
Fusion of gametes - In sexual reproduction the offspring inherit some characteristics from each parent anc are therefore different from both of them. Which gametes fuse is random and adds to the variety of the offspring produced.

Genetic - eg blood group A, B, AB or O.
Environmental - eg food and water availability, sunlight, rainfall, temperature. the frequency goes on Y and the independent variable on X. After plotting, we usually obtain a bell shaped curve, called a normal distribution curve. 
The mean is a measurement at the maximum height of that curve, giving us an average.
Standard deviation is a measurement of the width of the curve. It gives us an indication of the values on each side. 68% of measurements are given in 1 standard deviation, and 95% in 2 S.D's. The calculation for standard deviation is:
Standard deviation = √∑(x-x̅)²
                                   ¯¯¯n¯¯¯¯  
 ∑ = the sum of
 X = measured value from the sample
x̅ = the mean value
n = total number of values in the sample. 

Individual nucleotides are made up of 3 components:
1. a sugar called deoxyribose
2. a phosphate group
3. an organic base belonging to one of two groups:
- single ringed Cytosine (C) or Thymine (T)
- double ringed Adenine (A) or Guanine (G) 

They join together by a condensation reaction and form a mononucleotide. Two mononucleotides can in turn be joined by a condensation reaction between the sugar of one nucleotide and the phosphate of the other, to form a dicucleotide. Many nucleotides joining in this way produces a long chain called a polynucleotide. 

Organic base pairing:
Adenine always pairs with Thymine by two hydrogen bonds.
Cytosine always pairs with Guanine by three hydrogen bonds. 

DNA is the hereditary material that is responsible for passing genetic information from cell to cell and through generations. In total, there are around 3.2 billion base pairs in the DNA of a typical mammalian cell. It is adapted for its function because:

- It is very stable and can pass from generation to generation without change,

- Its two separate strands are joined only with hydrogen bonds, which allow them to separate during DNA replication and protein synthesis,

- It is an extremely large molecule and therefore carries an immense amount of genetic information,

- By having the base pairs within the helical cylinder of the sugar-phosphate backbone, the genetic information is protected from corruption by chemicals and physical forces.

The triplet code
That is the suggestion that a minimum of 3 bases code for each amino acid because:

- Only 20 amino acids occur regularly in proteins and each must have its own code of bases.
-Only four different bases are present in DNA and if each base coded for a different amino acid, only 4 different amino acids could be coded for. 
-Using a pair of bases, 16 different codes are possible which is still inadequate.
- Three bases produce 64 different codes, more than enough to satisfy the 20 amino acid requirement.

Some amino acids have more than one code. In eukaryotes, not much DNA is actually code for amino acids. 

In prokaryotic cells, like bacteria, DNA molecules are smaller, circular and are not associated with protein molecules, and therefore do not have chromosomes.
In eukaryotic cells, the DNA molecules are larger, form a line (are linear) and occur in association with proteins and form chromosomes. 
A chromosome consists of two threads joined at in the middle. The threads are called chromatids and the centre is called the centromere. The chromosomes are only visible when the cell is dividing. 
Although the number of chromosomes in a normal individual of a species is the same, the number between species can vary. The number of chromosomes in the cells of a normal individual is called the diploid number. The diploid number in humans is 46. The number is even because chromosomes occur in pairs called homologous pairs. In gametes, the diploid number is halved with 23 chromosomes in each. Half the diploid number is called the haploid number, in humans, 23. 
Genes occur in two, sometimes more, forms called alleles. For example, the gene for hair colour can be a brown (B) or blonde allele (b). 

Two ways: 
-Meiosis,
-Mitosis. 
Meiosis produces gametes (sperm and egg cells) that contains the haploid number of chromosomes so when they fuse to form a zygote, it contains the diploid number of chromosomes.  
During meiosis 1, the homologous chromosomes pair up and their chromatids wrap round each other. Equivalent portions of these chromatids may be exchanged during a process called crossing over. By the end of meiosis 1, the homologous pairs have separated with one pair from each going into one of the two daughter cells produced here. 
In meiosis 2, the chromatids move apart. At the end of this stage, four daughter cells have been formed. In humans, each of these cells contain 23 chromosomes.
Meiosis also brings about genetic variation by recombination of homologous pairs by crossing over (where alleles swap between chromosomes because they are close in their pairs) and by independent segregation (when the pairs move apart randomly and into the new gametes produced).

Selective breeding, or artificial selection involves identifying individuals with the desired characteristics and using them to parent the next generation. Offspring that do not exhibit the desired characteristics are killed or prevented from breeding. In this way, alleles for unwanted characteristics are bred out of the population. the variety of alleles in the population is deliberately restricted to a small of number of the desired alleles. This reduces genetic diversity. 

Selective breeding is often carried out in order to produce high-yielding breeds of domesticated animals and strains of plants. For example, in plants such as wheat, the features selected include large grains and a high gluten content, short stems and resistance to disease. 

The haemaglobins are a group of chemically similar molecules found in a wide variety of organisms. The structure of a haemaglobin is made up as follows:

-Primary structure, consisting of four polypeptide chains.
-Secondary structure, in which each of these polypeptides are coiled into a helix.
-Tertiary structure, in which each polypeptide chain is folded into a precise shape - an important factor in its ability to carry oxygen.
-Quarternary structure, in which all four polypeptides are linked together to form an almost spherical molecule. Each polypeptide is associates with a haem group - which contains a ferrous (Iron, Fe2+) ion. Each ion can combine with a single oxygen O2 molecule making a total of four molecules that can be carried by one single haemaglobin molecule in a human.

Haemaglobin is to transport oxygen. To be efficient at this, haemaglobin must:
-Readily associate with oxygen at the surface where gas exchange takes place,
-Readily dissociate from oxygen at those tissues requiring it. 

Let's look at the different haemaglobins at each end of a range:
- Haemaglobins with a high affinity to oxygen take up oxygen more easily but release it less readily. High affinity, low metabolic rate, not much movement. For example, a foetus.
-Haemaglobins with a low affinity to oxygen take up oxygen less easily but release it more readily. Low affinity, high metabolic rate, lots of movement. For example, a cheetah. 

When oxygen and haemaglobin combine, this it called loading or association. This occurs in humans in the lungs. 
When haemaglobin releases oxygen, it is called unloading or dissociation. This occurs in humans in the tissues. 

Starch:
Found in plants in small grains. It is chains of alpha-glucose joined by condensation reactions. The unbranched chain is wound into tight coils that makes it very compact. Starch is used for energy storage because:
it is insoluble and does not tend to draw water into the cells, preventing osmotic lysis.
-being insoluble, it does not easily diffuse out of cells,
-it is compact, so a lot of it can be stored in a small space
-when hydrolysed it forms alpha-glucose, which is both easily transported and readily used in respiration.  Starch is not in animal cells. We have glycogen.
Glycogen:
it is very similar to starch but forms shorter chains and is highly branched. It is stored as small granules mainly in the muscles and liver. Its structure suits it for storage for the same reason as starch, however because of its branches, it is more readily hydrolysed to alpha-glucose. Glycogen is never found in plant cells. 

Cellulose:
It differs from starch and glycogen because it is made of monomers of beta-glucose, not alpha. This seemingly small variation produces fundamental differences in the structure and function of this polysaccharide. The main reason for this is that in the beta-glucose units, the position of the -H group and the -OH group is reversed. This means that to form glycosidic bonds, each beta-glucose molecule must be rotated by 180 degrees compared to its neighbour. This results in the CH2OH group alternative between being above and below the chain. Rather than being coiled, cellulose is straight and is unbranched. The chains run parallel to each other allowing hydrogen bonds to form. Alone, hydrogen bonds add very little to strength by the overall number makes a considerable contribution to the strength of cellulose. Cellulose is for structure, not storage, It is the main component of plant cell walls. It also prevents the cell from bursting as water enters by osmosis. 

A leaf palisade cell is a typical plant cell. Its function is to carry out photosynthesis. Its main functions include:
-long, thin cells that form a continuous layer to absorb sunlight,
-numerous chloroplasts that arrange themselves in the best positions to collect the maximum amount of light,
-a large vacuole that pushes the cytoplasm and chloroplasts to the edge of the cell. 
Chloroplasts vary in shape and size but are typically disc-shaped. Their main features are:
-The chloroplast envelope is a double plasma membrane that surrounds the organelle. It is highly selective in what it allows to enter and leave the chloroplast.
-The grana are stacks of up to 100 disc-like structures called thylakoids. Within the thylakoids is the photosynthetic pigment called chlorophyll. Some thylakoids have tubular extensions that join up with thylakoids in adjacent grana. The grana are where the first stage of photosynthesis takes place. 
-The stroma is a fluid-filled matrix where the second stage of photosynthesis takes place. Within the stroma are a number of other structures, likes starch grains.  

Chloroplasts are adapted to their function of harvesting sunlight and carrying out photosynthesis in the following ways:
-The granal membranes provide a large surface area for the attachment of chlorophyll and enzymes that carry out stage 1 of photosynthesis.
-The fluid of the stroma possesses all the enzymes needed to carry out the seconds stage of photosynthesis. 
-Chloroplasts contain both DNA and ribosomes so they can quickly and easily manufacture some of the proteins needed for photosynthesis.

Characteristics of all plant cells, the cell wall consists of microfibrils of the polysaccharide cellulose in the matrix. Cellulose microfibrils have considerable strength and so contribute to the overall strength of the cell wall. They have the following features:
-They consist of a number of polysaccharides, such as cellulose.
-There is a thin layer, called the middle lamella which marks the boundaries between adjacent cell walls. 

The functions of the cellulose cell wall are:
-To provide mechanical strength in order to prevent the cell bursting under the pressure created by the osmotic entry of water,
-To give mechanical strength to the plant as a whole,
-To allow water to pass along is and so contribute to the movement of water through the plant.

The xylem is inside, the phloem is on the outside. Plants constantly lose water by transpiration and so the water must be replaced by the absorption through root hairs. They are efficient surfaces for exchange because:
-they provide a large surface area as they are very long extensions and occur in thousands on each branch of a root,
-they have a thin surface layer (the cell-surface membrane and the cellulose wall), across which matericals can move easily.

After absorption, water must continue by either the apoplastic or the symplastic route. 

Apoplastic:
Goes through the cell walls. This creates little or no resistance and is much faster than the symplastic route.

Symplastic route:
-Water enters by osmosis and increases the water potential of the root hair cell.
-The RHC now has a higher potential than the cell next it, so the water moves into the next cell.
-Water continues to move through the cell walls into its neighbouring cell because of potential different. This also causes a decrease in water potential in the cell that the water has just left, causing a pull of more water in to the previous cell wall.
-the water is filtered by the cytoplasm.
When the water reaches the casparian *****, filtered water (from the symplastic route) passes through and continues, but the water from the apoplastic route is forced into the symplastic route to be filtered so it can pass through. 

The concept of species:
-They are similar to one another but different from members of other species because they have similar genes and closely resemble each other, despite variation in alleles that causes genetic diversity. Eg, humans all have two eyes, but some are blue, some are brown, some are green.
-they are capable of breeding to produce, living fertile offsrping.

Species are named by the binomial system. This features:
-It is a universal system based upon Latin or Greek names.
-the first name is the generic name, denotes the genus to which the organism belongs. This is equivalent to the surname used to identify people and shared by their close relatives.
-The second name, the specific name denotes the species to which the organism belongs, like a first name, however unlike humans, it is never shared by other species within the genus. 
-The names are printed in itallics (or underlined if hand written) to indicate they are scientific names.
-The genus is capital and the species is lower case; Canis lupus.

Taxonomy is the study of groups and their positions in a hierachical order, where they are commonly known as taxonomic ranks, like a wolf is an animal, animalia. Here is the classification of a grey wolf.
Kingdom - Animalia 
Phylum - Chordata
Class - Mammalia
Order - Carnivora
Family - Canidae
Genus - Canis
species - lupus 

There are 5 domains:
-Animalia
-Plantae
-Fungi
-Protoctista
-Prokaryota  

Coutship behaviour helps to increase survuval chance by enabling individuals to:

-Recognise members of their own species to ensure that mating only takes place between the same species, because two species cannot produce fertile offspring.

-Identify a mate that is capable of breeding because both partners need to be sexually mature, fertile and receptive to mating

-Form a pair bond that will lead to successful mating and raising of offspring.

-Synchronise mating so that it takes place when there is the maximum probability of the sperm and egg meeting.  

Mutations are changes in DNA that result in different characteristics. Mutations arise in many ways. For example, one or more bases in a DNA sequence may be added deleted or replaced by others during replication. 

Conjugation occurs when one bacterial cell transfers DNA to another bacterial cell. It takes place as follows:
-One cell produces a thin projection that meets another cell and forms a thin conjugation tube between the two cells.
-The donor cell replicates one of its small circular pieces of DNA (plasmid).
-The plasmid is broken to make it linear before it passes along the donor's DNA to be transferred.
-In this way, the recipient cell acquires new characteristics from the donor cell. 

One way antibiotics work is by preventing bacteria from making normal cell walls. Water constantly enters bacterial cells by osmosis. This would normally cause the cell to burst by osmotic lysis. It doesn't burst because of the wall that surrounds all bacterial cells. This wall is made of peptidoglycan. It is tough and rigid and not easily stretched. Antibiotics attacks the peptidoglycan cell walls and prevents it from making them normally. Weakened walls means they are unable to withstand the pressure from the water entering uncontrollably, so osmotic lysis occurs, making the cells burst and thus die. 

Antibiotic resistance happens by mutation, and it then finds its way into new species of bacteria by horizontal gene transfer. This most commonly happens in hospitals; many patients, many different diseases, many types of bacteria, many types of antibiotic, much horizontal gene transfer, much resistance, creating super-bugs.

Biodiversity refers to the variety in the living world. It refers to the number and variety of living organisms in a particular area and has 3 components:
-Species diversity which refers to the number of different species and the number of individuals in that species within any one community.
-Genetic diversity which refers to the variety of genes possessed by the individuals that make up one species.
-Ecosystem diversity which refers to the range of different habitats within one particular area. 

Species Diversity Index, or Simpson's Diversity Index, or SDI is a calculation to measure species diversity. It is calculated as follows:
d = N(N-1)
¯∑¯n(n-1)¯¯¯ 

d= SDI
N = total number of organisms of all species
n = total number of organisms of each species
∑ = the sum of