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.

3.4.4 genetic diversity and adaptation

Genetic similarities and differences between organisms can be defined in terms of variation in DNA. This is because if is differences in DNA that lead to genetic diversity.

It is important to understand that al members of the same species have the same genes, which phenotype they express depends on which alleles they possess. Organisms of the same species differ in alleles (not genes!).

Genetic diversity is the total number of different alleles in a population (a population is a group of individuals of the same species in the same habitat at the same time). A species consists of one or more populations, The greater the number of different alleles that all members of a species possess the greater the genetic diversity of that species. This is important as it increases the chance of survival with environmental change as there is a greater probability that an individual will possess a characteristic that suits it to the new environment.

I must add that it is not equally likely that all alleles of a population are to be passed on. This is because not all individuals are reproductively successful so not all pass on their alleles. Differences between the reproductive success of individuals affects allele frequency within populations because:

• within any population of a species there will be a gene pool containing a wide variety of alleles
• random mutation may result in a new allele
• in certain environments the new allele might give its possessor an advantage over the other individuals
• this individual is better adapted so more likely to survive in their competition with others
• these individuals therefore have a better chance of successfully breeding and producing offspring
• only individuals that reproduce successfully will pass on their alleles to the next generation
• over time the frequency of the 'better' allele will increase whilst the 'worse' allele will decrease

This is the principle of natural selection. Natural selection results in species that are better adapted to the environment they live in. these adaptions may be:

• physiological
• to do with like inside stuff (e.g oxidization of fat rather than carbohydrate produces more water in kangaroo rats)
• behavioural
• to do with behaviour
• anatomical
• to do with anatomy

Types of selection

Directional selection

Process covered in 3.7.3

We need to know an example of this by antibiotic resistance in bacteria:

• A spontaneous mutation occurs in the allele of a bacterium that enables it to make a new protein
• this protein is an enzyme that breaks down an antibiotic before it's able to kill the bacterium
• the antibiotic was used to treat an individual and the bacterium was present
• the mutation gave the bacterium an advantage and it was not killed (unlike the rest of the population
• the bacterium that survived reproduced by binary fission and a built up a population of antibiotic-resistant bacteria
• the populations normal distribution curve shifted in the direction of a population having greater resistance to the antibiotic

Stabilising selection

Process covered in 3.7.3

The example we need to know of this is human birth weights. There is a much greater risk of infant mortality if the baby is born outside the 2.5-4.0kg range

3.4.3 Genetic diversity can arise as a result of mutation of during meiosis

Gene mutations involve a change in the base sequence of chromosomes. They can arise spontaneously during DNA replication and include base deletion and base substitution. Due to the degenerate nature of the genetic code, not all base substitutions cause a change in the sequence of encoded amino acids. Mutagenic agents can increase the rate of gene mutation. Mutations in the number of chromosomes can arise spontaneously by chromosome non-disjunction during meiosis.

Meiosis
Meiosis produces four daughter cells each with half the number of chromosomes as the parent cell. It is important as it (usually) produces gametes which have half the number of chromosomes which means the chromosome number of offspring does not double when two gametes fuse. During meiosis homologous pairs of chromosomes separate so only one chromosome from each pair enters a daughter cell (the haploid number). when two haploid gametes fuse during fertilisation the diploid/full number of chromosomes is restored. Meiosis involves two nuclear divisions (it's a bit like mitosis, but twice if you get me):

1. meiosis 1: homologous chromosomes pair up and their chromatids wrap around each other. Equivalent portions of these chromatids may be exchanged in a process known as crossing over. By the end of the is division the homologous pairs have separated with one chromosome from each pair going into one of two daughter cells
2. meiosis 2: the chromatids move apart and form 2 new cells. At the end of meiosis 4 cells have formed each with a diploid number of chromosomes

Meiosis also produces genetic variation among the offspring which may lead to adaptations that improve survival chances. It brings about genetic variation in the following ways:

• independent segregation of homologous chromosomes
• during meiosis 1 each chromosome lines up alongside its homologous partner at the equator, this arrangement is random. Which pair goes into each daughter cell with which other pairs depends on how they are lined up in the parent cell. Since the line up is random the combination of chromosomes that go into each cell is a matter of chance. This is called independent segregation.
• To further this, the alleles of each member of a homologous pair may differ. The independent assortment of these chromosomes produces new genetic combinations
• new combinations of maternal and paternal alleles (crossing over and recombination)
• after each chromosome lines up alongside its homologous partner the chromatids of each pair become twisted around one another. During this time tensions are created and portions of the chromatids break off. They then rejoin with the chromatids of its homologous pair. In this way new genetic combinations of maternal and paternal alleles are produced.
• If there is no recombination by crossing over only two different types o cell are produced. If recombination occurs four different types are produced. This means that crossing over further increases genetic variety.

As we know, homologous pairs line up at the equator during meiosis 1. Each of one pair can pass into each daughter (independent segregation) so there is a large number of possible combinations of chromosomes in any daughter cell. we can use the formula 2ⁿ where n is the number of pairs of homologous chromosomes to determine the number of possible combinations of chromosomes for each daughter cell.

Variety further increases through the random pairing of male and female gametes. We can calculate the number of combinations using the equation (2ⁿ)².

NOTE: It is important to realise that these calculations are based on chromosomes that do not undergo crossing over. If recombination occurs it will greatly increase the number of possible combinations in the gametes.

3.4.2 DNA and protein synthesis

3.4.2 DNA and protein synthesis 

The genome is the complete set of genes in a cell and the proteome is the full range of proteins that a cell is able to produce. 

We need to be able to recall and talk about the structure of mRNA and tRNA.

RNA overall:

• pentose sugar (ribose)
• A, U, C, G
• a phosphate group
• a polymer made up of repeating mono nucleotide sub-units
• single stranded

mRNA:

• small enough to leave the nucleus through clear pores to enter the cytoplasm
• it contains coded information to determine the sequence of amino acids in the proteins which are synthesised
• a codon is a sequence of three bases on mRNA that codes for a single amino acid
• long strand arranged in a single helix (1,000s of nucleotides)
• base sequence determined by the base sequence of a length of DNA (transcription)
• associated with ribosomes in the cytoplasm
• acts as a template for protein synthesis

tRNA:

• relatively small (around 80 nucleotides)
• single stranded chain folded into a clover-leaf shape with one end of the chain extending beyond the other
• an amino acid can easily bind to this extending part (there are many different types of tRNA, each is specific to a different amino acid)
• on the other end is an anticodon (sequence of three bases) this binds with the codon during protein synthesis (the codon and anticodon are complimentary).

Transcription

This is the process of making pre-mRNA from DNA (the DNA acts as a template):

• an enzyme acts on a specific region of the DNA causing the two strands to separate exposing the nucleotide bases in that region
• the nucleotide bases on one of the two DNA strands (this is the template strand) pair with complimentary free nucleotides by complimentary base pairing
• RNA polymerase moves along the strand joining the nucleotides together forming a pre-mRNA molecule
• the DNA strand rejoins behind the pre-mRNA strand
• when the RNA polymerase reaches a particular sequence of bases (a stop triplet code) it detaches and the production of pre-mRNA is complete

Splicing

In prokaryotes transcription results directly in the production of mRNA from DNA. In eukaryotic cells transcription results in pre-mRNA which must be spliced to form mRNA. The DNA of a gene of eukaryotic cells is made up of sections known as exons (coding) and introns (non-coding). Introns prevent polypeptide synthesis, so we must remove these and join the exons together. This process is known as splicing. The mRNA molecule now leaves the nucleus via a nuclear pore.

Translation

• A ribosome becomes attached to the start codon at one end of the mRNA molecule
• the tRNA molecule with the complementary anticodon moves to the ribosome and pairs up with the codon on the mRNA. This tRNA carries a specific amino acid
• A tRNA molecule with a complementary anticodon binds to the next codon
• the ribosome moves along the mRNA bringing together the two tRNA molecules
• the two amino acids are joined by a peptide bond using ATP which is hydrolysed to provide the energy required
• the ribosome moves onto the next codon and the first tRNA is released from its amino acid (simultaneously)
• this tRNA is now free to collect another amino acid
• this continues until the ribosome reaches a stop codon
• here the ribosome, mRNA, and last tRNA molecule all separate and the polypeptide chain is complete

3.2.3 Transport across cell membranes

Okay so the basic structure of cells is covered in 3.2.1.1 and 3.1.1.2. Here, I will cover the arrangement/movement/structure of the cell surface membrane:

• phospholipids
• hydrophilic heads point outward and hydrophobic tails point inward creating a phospholipid bilayer
• lipid soluble material moves through the membrane via this bilayer
• this bilayer:
• allows the movement of lipid-soluble material
• prevents water-soluble substances entering/leaving
• makes the membrane flexible and self-sealing
• proteins
• These are interspersed throughout the cell surface membrane embedded in the phospholipid bilayer in two main ways:
• some occur in the surface of the bilayer and never extend completely across it. These either act to give mechanical support to the membrane or (in conjunction with glycolipids) as cell receptors for molecules such as hormones
• others span the membrane. Protein channels form water-filled tubes to allow water-soluble ions to diffuse across whilst protein carriers bind to ions/molecules and change shape in order to move these molecules across the membrane.
• provide structural support
• allow active transport (carrier proteins)
• act as channels to transport water-soluble substances across (channel proteins)
• form cell-surface receptors for identifying cells
• help cells adhere to each other
• act as receptors (e.g for hormones)
• glycoproteins
• carbohydrate chains attached to many extrinsic proteins on the outer surface of the cell membrane
• act as cell-surface receptors for hormones and neurotransmitters
• help cells attach to one another forming tissues
• allow cells to recognise one another e.g lymphocytes can recognise an organism's own cells
• glycolipids
• made up of carbohydrate covalently bonded with a lipid. The carbohydrate section extends into the phospholipid bilayer where it acts as a cell-surface receptor for specific chemicals
• act as recognition sites
• help to maintain the stability of the membrane
• help cells to attach to one another forming tissues
• cholesterol
• this restricts the movement of other molecules making up the membrane
• the fluid-mosaic model
• the way in which the various molecules are combined into the structure of the cell-surface membrane is known as the fluid-mosaic model:
• fluid because the individual phospholipid molecules can move relative to one another giving the membrane a flexible structure that is constantly changing shape
• mosaic because the proteins that are embedded in the phospholipid bilayer vary in shape/size/pattern similar to the tiles of a mosaic

The permeability of the cell-surface membrane is as follows. Substances can't enter if they are:

• not soluble in lipids (cannot pass through bilayer)
• too large (cannot pass through channels)
• of the same charge (they will be repelled)
• electrically charged (this means they are polar). In this case they have difficulty passing through the non-polar hydrophobic tails in the phospholipid bilayer

Movement across membranes occurs by: 
• simple diffusion (involving limitations imposed by the nature of the phospholipid bilayer) 
• facilitated diffusion (involving the roles of carrier proteins and channel proteins) • osmosis (explained in terms of water potential) 
• active transport (involving the role of carrier proteins and the importance of the hydrolysis of ATP)
• co-transport (illustrated by the absorption of sodium ions and glucose by cells lining the mammalian ileum). 

Simple diffusion
This is 'the net movement of molecules or ions from a region where they are more highly concentrated to one where their concentration is lower until evenly distributed'. It is a passive process

Facilitated diffusion
So we know that only small non-polar molecules can diffuse across the cell-surface membrane. The movement of charged ions and polar molecules is facilitated by protein channels and carrier proteins. It only occurs at specific points along the membrane (where these proteins are situated) and, like simple diffusion, also occurs down a concentration gradient. It is also passive.

• Protein channels form water-filled hydrophilic channels across the membrane that allow specific water-soluble ions to pass through. They are selective and open in the presence of a specific ion (in this way they have control of entry/exit of substances in/out of the membrane). The ion binds to the protein causing it to change shape in a way that closes it to one side of the membrane and opens it to the other side.
• Carrier proteins bind with a specific molecule (e.g glucose) and change their shape in such a way that the molecule is released to the inside of the membrane.

Osmosis
This is 'the passage of water from a region where it has a higher water potential to a region where it has a lower water potential through a electively permeable membrane'. It is important to realise that the highest value water potential can be is 0kPa (pure water) and anything not pure water has a negative water potential. Osmosis is essentially the diffusion of water molecules. 

In animal cells, when water enters the cell swells and bursts, when water leaves the cell shrinks. In plant cells when water enters the cell becomes turgid, when water leaves the shell becomes plasmolysed (at the same water potential the condition is incipient plasmolysis).

Active transport
This is 'the movement of molecules or ions into or out of a cell from a region of higher concentration to a region of lower concentration using ATP and carrier proteins'. ATP is used to directly move molecules/individually move molecules using a concentration gradient which has already been set up by direct active transport (this is co-transport):

• the carrier proteins that span the membrane bind to a molecule/ion (the molecule/ion binds to the receptor site)
• on  the inside of the cell/organelle ATP binds to the protein causing it to split into ADP + Pi. This causes the protein molecule to change shape opening to the opposite side of the membrane
• the molecule/ion is released to the other side of the membrane
• the phosphate molecule is released from the protein which causes the protein to revert to its original shape

Co-transport 
Sometimes more than one molecule/ion may be moved in the same direction at the same time by active transport. Occasionally a molecule/ion is removed at the same time one is assed. An example of this is the sodium-potassium pump. Sodium ions are actively removed from the cell/organelle while potassium ions are actively taken in from the surroundings.


Cells may be adapted for rapid transport across their internal or external membranes by an increase in surface area of, or by an increase in the number of protein channels and carrier molecules in, their membranes. 


Differences in.....

• increased surface area = larger area for diffusion
• increased number of channel/carrier protein = more placed for facilitated diffusion/active transport to occur
• a larger difference in concentration gradient/water potential means a faster rate of transport

......and vice versa.

3.2.2 All cells arise from other cells

Eukaryotic organisms
In multicellular organisms not all cells retain the ability to divide. Eukaryotic cells that to retain the ability to divide show a cell cycle. Cell division can occur by mitosis or meiosis. Mitosis produces two daughter cells that have the same number of chromosomes as the parent. We will cover mitosis in this section. Meiosis produces four daughter cells each with half the number of chromosomes of the parent cell. Meiosis is covered in section 3.4.3.

Mitosis can be split into 5 stages:

Interphase
Mitosis is proceeded by a period during which the cell is not dividing (this is interphase). Here, DNA replication occurs. The two copies of DNA remain joined at the centromere.
Prophase

• Chromosomes first become visible by shortening and condensing
• (in animals) centrioles move to opposite ends/the poles of the cell
• spindle fibres develop from each centriole. These span the cell from pole to pole and are collectively called the spindle apparatus.
• the nucleolus disappears and the nuclear envelope breaks down leaving the chromosomes free in the cytoplasm.
• the chromosomes are drawn towards the equator by spindle fibres attached to the equator

Metaphase

• the chromosomes can now be seen to be made up of two chromatids (each an identical copy of the DNA from the parent cell unless mutation occurs)
• chromosomes arrange themselves along the equator of the cell

Anaphase

• centromeres divide in two and spindle fibres pull the individual chromatids apart
• chromatids more to their respective poles and are now referred to as chromosomes (energy provided by mitochondria situated around the centrioles)

Telophase (+ cytokinesis)

• chromosomes reach their respective poles and become longer and thinner and disappear altogether leaving widely spread chromatin
• spindle fibres disintegrate

NOTE: Mitosis is a controlled process. Uncontrolled cell division can lead to the formation of tumours and of cancers. Many cancer treatments are directed at controlling the rate of cell division.

We need to be able to calculate mitotic index:

mitotic index = number of cells in mitosis x 100 / total number of cells

Prokaryotic cells
These divide by binary fission:

• The circular DNA molecule replicates and both copies attach to the cell membrane
• the plasmids replicate (a variable number)
• the cell membrane begins to grow between the two DNA molecules and begins to pinch inward, dividing the cytoplasm in two
• a new cell wall forms between the two molecules of DNA dividing the original cell into two identical daughter cells (each with a single copy of the circular DNA and a variable number of copies of the plasmids).

Viruses

Viruses do not undergo cell division. They inject their nucleic acid into a host cell infecting it. The host cell replicates the viral particles.

3.2.1.2 Structure of prokaryotic cells and of viruses

Prokaryotic cells
Prokaryotic cells are much smaller than eukaryotic cells. They also differ from eukaryotic cells as they:

• lack membrane-bound organelles
• have smaller (70S) ribosomes
• have no nucleus (instead they have a single circular DNA molecule that is free in the cytoplasm and not associated with proteins)
• a cell wall containing murein (a glycoprotein)

Some prokaryotic cells might additionally have:

• one or more plasmids
• a capsule surrounding the cell
• one or more flagella

Viruses
These are acellular non living particles. They are smaller than bacteria (20-300nm) and contain nucleic acids (DNA or RNA) as genetic material. They can only multiply inside a host cell. The nucleic acid is enclosed in a protein coat (a capsid). Some viruses are further surrounded by a lipid envelope (e.g HIV). The lipid envelope/capsid has attachment proteins which allow the virus to identify and attach to a host cell.

3.2.1.3 Methods of studying cells Content

This section is all about microscopes. The material we put under the microscope is the object, the appearance of this material when viewed under the microscope is the image. The magnification of an object is how many times bigger the image is when compared to the object:

magnification = size of image / size of object

NOTE: remember to keep the units of measurement the same!

Resolution is different to magnification. The resolution of a microscope is the minimum distance apart that two objects can be in order for them to appear as separate items. The resolving power depends on the wavelength/form of radiation emitted from the microscope. Increasing the magnification will increase the size of an object but not necessarily the resolution (every microscope has a limit resolution).

Okay so there are three types of microscope we use to study cells: the optical/light microscope, the transmission electron microscope, and the scanning electron microscope. We need to know the principles and limitations of using each one:

• The light microscope
• can only distinguish between objects more than 2μm apart due to the long wavelength of light.
• the transmission electron microscope
• can be focused by electromagnets as electrons are negatively charged
• can resolve objects that are just 0.1nm apart
• beams pass through a thin section of the specimen. Parts of this specimen absorb electrons and appear darker (other parts allow the electrons to pass through and so appear bright)
• an image is produced on a screen which can be photographed to produce a photomicrograph
• the resolving power (0.1nm) cannot always be achieved due to difficulties in preparing the specimen/the high energy electron beam may destroy the specimen
• the main limitations are as follows:
• whole system must be in a vacuum (living specimens cannot be observed)
• image produced is black and white
• a complex staining process is required
• specimen must be extremely thin
• image may contain artefacts
• 2D image produced
• the scanning electron microscope
• can be focused by electromagnets as electrons are negatively charged
• can resolve objects that are 20nm apart
• directs a beam of electrons on to the surface of the specimen from above (rather than penetrating from below). The beam is passed back and forth across a portion of the specimen in a regular pattern - the electrons are scattered depending on the contours of the specimen surface.
• A 3D image is produced by computer analysis of the pattern of scattered electrons and secondary electrons produced.
• the main limitations are as follows:
• whole system must be in a vacuum (living specimens cannot be observed)
• image produced is black and white
• a complex staining process is required
• image may contain artefacts

Cell fractionation
This is used to obtain large numbers of isolated organelles. It is the process whereby cells are broken up and the different organelles are separated out. Before cell fractionation can occur the tissue is placed in a cold buffered solution of the same water potential. this is because:

• cold to reduce enzyme activity that might break down the organelles
• is of the same water potential to prevent organelles bursting/shrinking as a result of osmotic gain/loss of water
• buffered so that the pH does not fluctuate.

The two stages of cell fractionation are homogenation and ultracentrifugation:

• homogenation
• cells are broken up by a homogeniser which releases the organelles from the cell. The resultant fluid is known as a homogenate and is filtered to remove any complete cells/large pieces of debris
• ultracentrifugation
• this is the process by which the fragments in the filtered homogenate are separated in a machine (a centrifuge). this spins the tubes of homogenate at very high speeds which creates a centrifugal force:
• the tube of filtrate is placed in the centrifuge and spun at slow speeds
• the heaviest organelles are forced to the bottom and form a pellet
• the supernatant is removed
• the supernatant is transferred to another tube and spun in the centrifuge at a faster speed than before
• the next heaviest organelles are forced to the bottom
• etc