AS Biology, topic 4

The Genetic code is the sequence of codons in mRNA, which code for specific amino acids. In the code, each codon is read in sequence, seperate from the triplets before and after. The code is non-overlapping, as base-triplets don't share their bases

It's degenerate, as there are more combonations of triplets (64) than amino acids (20), meaning that some amino acids aare coded for by more than one base triplet. Some triplets (at the start and end of mRNA) are start/stop signals, as they tell the cell when to start/stop producing a protein

The code is universal; the same specific base triplets code from the same amino acids in all living things

• Genes are a section of DNA containing coded information for making polypeptides and fRNA. The gene is in the form of a specific sequence of bases along the DNA molecule
• Genes are responsible for the organism's development and activities, as they determine the proteins (many of which are enzymes that control chemical reactions) that are produced.
• Genes are located in a particular position (locus) on the DNA molcule, and code for: the amino acid sequence of a polypeptode or functional RNA- tRNA, mRNA
• One DNA molecule contains many genes

Whilst DNA's structure doesn't differ between organisms, it is stored differently in eu/prokaryotic cells:

Nuclear Eukaryotic DNA is linear and associated with proteins:

• Linear DNA molecules that exist as chromosomes; thread-like structures, each one made of one long DNA molecule. Chromosomes are found in the nucleus. DNA is very long, so has to be wound up to fit in the nucleus; it's wound around proteins called histones, which help to suppott the DNA. They're both then coiled up to make a compact chromosome.
• Mitochondria and chloroplasts also have DNA, but it's circular, shorter and not associated with histone proteins

DNA molecules are shorter and circular in Prokaryotes

• Here, the DNA is shorter and circular. Instead of it being wound around histones, it condenses to fit in the cell using supercoiling

• Genes are sequences of DNA bases that code for either a polypeptide or functional RNA (fRNA)
• The sequence of amino acids in the polypeptide is what forms a protein's primary structure. Different polypeptides have a different number/order of amino acids. This order is determined by the bases in a gene. Amino aicds are coded by a sequence of 3 bases in a gene (triplet)
• To make polypeptides, DNA is first copied into messenger RNA (mRNA) during the first stage of protein synthesis
• The genes that code code for polypeptides code for fRNA, which is RNA molecules other than mRNA that perform specific tasks during protein synthesis. E.g. tRNA and rRNA

A cell's genome is its complete set of genes. A cell's proteome is the full range of proteins that cell is able to produce

•  Most of this DNA codes for fRNA, but the eukaryotic DNA that does code for polypeptides contain sections within these genes that don't code for amino acids. These sections are known as introns, and there can be several within one gene. The sections coding for amino acids are called exons
• During protein synthesis, introns are removed so that they don't impact the amino aicd order. They're not found in prokaryotic DNA
• Sections of eukaryotic DNA contain multiple repeats, which repeat over and over without coding for amino acids. These are known as non-coding repeats

• Genes can exist as alleles. As each gene has a slightly different order of bases, they code for different versions of the same polypeptide. For example, the gene determining blood type exists as one of three alleles; one determining A, one B and one O:
• In the eukaryotic cell nucleus, DNA is stored as chromosomes in 23 homologus pairs. In a homologus pair, both chromsomes are the same size and have the same genes, but could have different alleles. Alleles coding for the same characteristics (e.g. blood type) are found at the same fixed position (locus) on each chromosome in a pair

RNA (Ribonucleic acid) is a polymer made of repeating mononucleotide sub-units, forming a single strand in which each nucleotide is made of: 

• the pentose sugar ribose, one of the organic bases- A, C, G, U and a phosphate group

There are 2 types of important RNA in protein synthesis:

• mRNA: made during transcription, carries the genetic code from the DNA to ribosomes, where it's used to make a protein. mRNA's bade sequence is determined by the sequence of bases in DNA during transcription. It's a single polynucleotide strand arranged in a single helix. mRNA processes info in the form of codons- the sequence of these determines the amino acid sequence of the subsequent polypeptide
• tRNA: a small, single-stranded chain with one end extending beyond the other- this is the amino acid binding site. At the opposite end is a specific sequence of 3 bases (an anticodon). Each tRNA (and anticodon) is specific to one amino acid. It's involved in translation and carries the amino acids that're used to make proteins to the ribosomes. It is folded into a clover shape that's held together by hydrogen bonds between the base pairs

Protein synthesis is the process by which proteins are made; the cytoplasm of each cell has the capacity to make every protein from 20 amino acids- which proteins are made depends upon the DNA in the cell's nucleus. Transcription is the process of making an mRNA copy, using part of the DNA as a template. It occurs in nucleus of eukaryotic cells, and cytoplasm of prokaryotes:

• RNA polymerase (enzyme, RNA P) attaches to the DNA double-helix at the start of a gene. The H2 bonds between the 2 strands break, causing them to separate and the DNA to uncoil, exposing the nucleotide strands
• One of these 2 strands is used as a template (TS) to make the mRNA copy- the RNA polymerase lines up free RNA nucleotides with the TS's exposed bases. They attach and due to complementary base pairing, the mRNA strand is a complementary copy of the DNA TS (but T is replaced with U). The bases are joined by RNA P, forming the mRNA molecule
• RNA P moves along the DNA, separating the strands and assembling mRNA, but DNA strands rejoin behind as new H2 bonds are formed, so only abut 12 base pairs are exposed at once. When RNA P reaches a stop signal, it stops making mRNA and detaches from the DNA
• In eukaryotes, mRNA moves out of the nucleus via a nuclear pore and attaches to a ribosome in the cytoplasm, where translation occurs

Transcription makes different products in eukaryotes and prokaryotes:

• In prokaryotes the intons and exons are both copied into mRNA during transcription; mRNA containing these is called 'pre-mRNA'. A process called 'spilicing' then occurs in which the introns are removed and the exons are joined together to form the mRNA strands. This occurs in the nucleus, and then the mRNA leaves for the cytoplasm to begin translation
• Spilicing doesn't take place in prokarotes as there are no introns in prokaryotic DNA. So, there mRNA is produced directly from the DNA

This occurs at the ribosomes in the cytoplasm in both eukaryotes and prokaryotes. The amino acids are joined together to make a polypeptide chain (protein), following the sequence of codons carried by the mRNA:

• The starting codon at one end of mRNA becomes attached to a ribosome and tRNA molecules carry amino acids to it. ATP provides energy for the amino acid and tRNA to bond
• The tRNA (carrying the amino acid) has a complementary anticodon sequence to the mRNA's anticodon and attaches itself via specific base pairing. A second tRNA molecule attaches itself to the next codon in the same way
• These 2 amino acids on the tRNA join by a peptide bond, using an enzyme and hydrolysed ATP. The first tRNA will move away, leaving its amino acid behins and is free to collect another one from the pool in the cell
• A 3rd tRNA bonds to the next mRNA codon and its amino acid bonds to the first 2. The 2nd tRNA then moves away. This continues, producing a polypeptide chain of linked amino acids, until there's a stop codon on the mRNA molecule. The chain will then move away from the ribosome, and translation is complete
• Sometimes a single polypeptide chain is a functional protein, but often multiple are linked together to form a quaternary structure, and the chain is folded/coiled

• DNA is passed down generation by gametes, which are sex cells; sperm and eggs. At fertilisation, they join together to form a zygote, which is then able to divide to form a new organism.
• Normal body cells have a diploid number (2n) (46) chromosomes, meaning each cell contains 2 of each chromosomes- one from mum and one from dad. But gametes have a haploid number (n) of chromosomes (23 in humans), as there's only one copy of each chromosome
• At fertilisation, a haploid sperm and egg fuse together to form a normal diploid cell, with half of the chromosomes coming from each parent
• During sexual reproduction, fertilisation is random; any sperm can fertilise any egg. This produces zygotes with different combinations of chromosomes to both parents, increasing the genetic diversity within the species

Gametes are formed by meiosis, which is a form of cell division that occurs in reproductive organs. It splits diploid cells into haploid cells, otherwise when the gametes fused, you'd get double the number of chromosomes:

• Before meiosis starts, the DNA unravels and replicates, producing 2 copies of each chromosomes (chromatids). Then condenses to form double-armed chromosomes, made from 2 sister chromatids that're joined in the middle by a centromere
• Meiosis 1 (1st division): chromosomes arrange each other into homologus pairs (the chromosomes making up each pair are the same size and have the same genes, but could have different alleles)
• The paird are separated, halving the chromosomes number
• Meiosis 2 (2nd division): sister chromatid pairs are separated via centromere division to produce 4 gametes that're genetically different

During meiosis I, 2 homologus pairs come together and pair up. The chromatids twist around each pther and swap over, so they still contan the same genes but a different combo of alleles. Equivalent portions are exchanged

Meiosis produces genetically different cells that leads to genetic variation during 2 events:

• Crossing over of chromatids in meiosis I means that each of the 4 daughter cells has chromatids with different alleles due to recombination (when the alleles of one chromatid break off and combine with another chromatid)
• Independent segregation of chromosomes: each homologus pair is made up of 1 maternal and 1 paternal chromosome. When the pairs are separated in meiosis I, it's random which chromosome from each pair will end up with each daughter cell, so they all have different combos of maternal and paternal, leading to genetic variation in offspring

Both of these proesses have different outcomes:

• Mitosis produces cells with the same number of chromosomes as parent cells, but meiosis produces daughter cells with half of the number
• Mitosis produces genetically identical daughter cells (to each other and the parent cells), meiosis produces genetically different cells
• Mitosis produces 2 daughter cells, whereas meiosis produces 4 

These are caused by errors in cell division. When meiosis works properly in humans, all 4 daughter cells end up with 23 whole chromosomes- 1 from each homologus pair (1-23). But if it goes wrong, cells can be produced with a varied number of whole chromosomes or parts of chromosomes. E.g. 2 daughter cells may be okay, but the other 2 could be muddled- one could have 2 chromosome 8s and the other one have none. This is known as 'chromosome mutation' and is due to errors is meiosis. It can lead to inhertited conditions, as errors are present in the gametes (hereditary cells)

One example of this is 'non-disjunction', which is when the chromosomes fail to separate properly. If this occurs to chromosome 21 in humans, it can lead to Down's Syndrome. This is caused by having an extra copy (or extra part) of chromosome 21. When the gamete with the extra copy fuses to another gamete at fertilisation, the zygote produced will have 3 copies of chromosome 21

• They're changes to DNA base sequence- errors include 'substitution', where one base is swapped with another, and 'deletion', where one base is deleted. Other errors can inc inserting, duplicating bases wtc.
• The order of DNA bases in a gene determines amino acid order, so mutations in a gene can change the protein that will be formed
• Not all mutations affect the order of amino acids- the genetic code is degenerate, so some amino acids are coded for by more than one DNA triplet, so not all substitution mutations wll change the amino acid sequence, as the triplets could code for the same amino acids
• But, deletions will always affect amino acid order, as it changes the number of present bases, causing a shift in all of the following base triplets
• Mutagenic agents increase the rate of mutations; depsite mutations occuring spontaneously, these agents (e.g. UV radiation and some chemicals and viruses) can increase the rate at which these mutations occur

Alleles are different versions of the same gene, and a number of different alleles of genes within a species/population creates genetic diversity. Genetic diversity within a population is increased by:

• Mutations in DNA, forming new alleles
• New alleles being introduced when individuals from a different population migrate and reproduce; this is called 'gene flow'

Genetic diversity is what allows natural selection to occur

This is an event that reduces a population, e.g. when lots of organisms die before reproducing, therefore reducing the number of different alleles in the genepool and the subsequent genetic diversity. Then, when the survivors reproduce, the larger population is created from fewer, less diverse, individuals.

The founder effect is an example of a genetic bottleneck, and is when just a few organisms from a population start a new colony, meaning there's only a few alleles in the initial gene pool. In the new colony, the frequency of these alleles may be very different to that in the initial population; orginially, certain alleles could have been rare, but in the new colony they could now be common. This can lead to high rates of genetic disease. This effect can be due to migration, leading to the geographical separation of the new colony from the orginial population

Mutations can create new alleles; if these are harmful, they'll often quickly die out. But helpful ones can improve the organism's ability to survive in an environment; these advantageous alleles are passed on through natural selection, becoming more frequent in populations:

• Individuals with alleles increasing survival are more likely to reproduce and pass on genes, meaning a higher proportion of the next generation will have the beneficial alleles and so on, so the frequency becomes greater with each generation. This eventually leads to evolution (gradual change in species over time), as the allele is more common in the population. Adaptation and selection are key factors in evolution

Adaptations help organisms survive in an environment in 3 ways:

• Behavioural adaptations- ways an organism acts to increase survival and reproduction chances
• Physiological adaptations- processes inside the organism increasing survival chances
• Anatomical adaptations- structural features on the organism's body that increase survival chances

Different types of natural selection affect allele frequency in different ways:

• Antibiotic resistance shows directional selection, which is when individuals with alleles for extreme characteristics are more likely to survive and reproduce, poss in response to environmental change. E.g. some individuals in a population have alleles allowing them to resist an antibiotic. If the population is exposed to the antibiotic, bacteria without the resistant allele will be killed, allowing the resistant bacteria to survive and reproduce without competition, passing on the resistance to offspring until most of the population has the allele
• Human birth weight shows stabalising selection, which is when individuals with alleles for characteristics towards the middle of the range are more likely to survive. Occurs when the environment isn't changing, reducing the range of poss characteristics. E.g. very small babies are less likely to survive as it's hard to maintain body temp, and for very big babies it's hard to give birth to them. Conditions are most favourable for medium-sized babies, so weight tends to shift towards the middle of the range

• Species- a group of similar organisms able to produce fertile offspring
• Hybrids- can be artificially bred, but can't produce fertile offspring

Phylogeny is the evolutionary study/history of groups of organisms, telling us who is related and how closely. All organisms have evolved from a common ancestor, and the links between them all can be shown on a phylogenetic tree. Closely related species are those that diverged away from each other the most recently. 

Taxonomy isthe science of classification; involes naming organisms and sorting them into groups, making them easier to identify and study. Scientists take phylogeny into account when classifying organisms, grouping them according to evolutinary relationships. There are 8 taxa in the system, which are arranged at a heirarchy with the largest groups at the top; organisms can only belong to one group at each level of the heirarchy, so there's no overlap. Organisms are first sorted into one of 3 domains; eukarya, bacterua and archaea. This is then followed by kingdom, phylum, class, order, family, genus, species As move down the heirarchy, there are more groups at each level with fewer organisms in each one. These organisms become more closely related as you go down.

Scientists constantly update classification systems due to new evidence about known organisms.

Binomial naming system- this is used to name classified organisms, by giving them one internationally accepted scientific name in Latin, with 2 parts. 1st part is the genus name and has a captal letter, 2nd part os the species name, and begins with a lower case letter. Names are always wrirren in italics, or underlines if handwritten. This system helps to avoid the confusion of using common names, as one common name can be used for many different species.

Courtship behaviour can be used to help classify species as it is species specific; only members of the same species will do and respond to that courtship behaviour. This helps members of the same species to recognise each other, preventing interbreeding and increasing the chance that fertile offspring will be produced. The more closely related the species, the more similar the courtship behaviour. E.g. fireflies give off pulses of light, and the sequence of the flashes is specific to each species.

• Genome sequencing- advances here allow the entire base sequence of an organism's DNA to be determined. This can be compared between organisms to determine how closely they're related. Closely realted species will have a higher percentage of similarity in theur DNA base order
• Comparing amino acid sequence- within a protein, this sequence is coded for by DNA base sequence. As this is more similar in realted organisms, they also have similar amino acid sequences in their proteins
• Immunological comparisons- similar proteins will also bind to the same antibodies, so you can compare the similarity of this too

Genetic diversity= the number of different alleles in a population. Previous estimates of this were made by looking at the frequency of measurable or observable characteristics n a population. As alleles determine different characteristics, a wide variety of each characteristic suggested a high number of different alleles and therefore genetic diversity. 

Now, new gene technologues can measure genetic diversity directly. Different alleles of the same gene have slightly different DNA base sequences; comparing the DNA base sequences of the same gene in different organisms allows scientists to find out how many alleles of that gene are in the population. Different alleles also produce slightly different mRNA base sequences, so proteins with differing amino acid sequences can be compared. 

Such technology gives more accurate and easy estimates of genetic diversity in a species/population

Variation exits both within and between species. It can be cause by genetic factors; different species have different genes, causing variation within specoes. Variation can also be caused by differences in environment, e.g. food. Most variarion within a species is caused by a combo of both. 

When measuring variation, samples should be taken and used as a model for the population. These samples have to be random to avoid bias- e.g. using a random number generator to pick the coordinates the sample will be taken from.

Samples are used to draw conclusions about the whole population, so they have to accurately represent the population and ensure the results aren't down to chance. A statistical test can be used to ensure the results are significant and therefore respresent the whole population

• Mean: you can use the mean to look for variation between samples. Once calculated uou can plot the meas on a graph; most samples will include values either side of the mean, producing a bell-shaped curve that indicates a normal distribution
• Standard deviation- tells you how values in a single sample vary by measuring their spread about the mean. Sometimes the mean is written as (e.g.) 9+- 3; so the mean is 9 and SD is 3, so most values are spread between 6 and 12
• Error bars- the SD can be plotted on a graph/chart displaying mean values using error bars. The top of the bar on the graph is the mean, and then the error bars extend 1 SD above and 1 below the mean (so its total length is twice the SD). The longer the bar is, the larger the SD and more spread out the data is from the mean

• Biodiversity= the variety of living organisms in an area. Areas with high biodiversity have lots of different species
• Habitat= the place an organism lives
• Community= all of the populations of different species in one habitat

Biodiversity can be considered on a range of scales, from local to gloal:

• Local biodiversity considers the variety of species in a small habitat that's local, e.g. a pond
• Global biodiversity is the variety of species on earth- recent estimates are around 8.7 million. Biodiversity varies in different parts of the world; it;s greatest at the equator and decreases towards the poles

• Species richness is a measure of the number of different species in a community. It can be calculated using random samples and counting the number of different species found within them. Species richness is also a measure of biodiversity. But, the number of different species in a community isn't the only thing that impacts biodiversity. The population sizes of species does too; larger populations within a community are more significant than smaller ones
• An index of diversity is another way of measuring biodiversity that takes both species richness and population size in a community into account. It's calculated using this formula: 

d = N (N-1)/sum of n(n-1)  N= total no of organisms of all specoes  n= total no of organisms in 1 species

The higher the number, the more diverse the area is. If all the individuals are of the same species, the biodiversity is 1

Many methods that maximise food produce can minimise biodiversity:

• Woodland clearace- done to increase area of farmland, but directly decreases the number of trees and different tree species. Also destroys habitats- some specoes can lose their shelter/food souece- can die or migrate, reducing biodiversity
• Hedgerow removal- increases farmland area by creating bigger field, but decreases biodiversity for the same reasons as above
• Pesticides- reduces biodiversity directly by killling 'pests'. Also, species that feed on them will lose a food source
• Herbicides- kills weeds, reducing biodiversity and poss no of organisms that feed on them
• Monoculture- when farmers have fields containing only 1 type of plant- supports fewer organisms 

Conservation schemes can help, e.g. by giving legal protection to endangered species, creating protected areas of land that resticts further development and 'The Environmental Stewardship scheme' that encourages farmers to conserve biodiversity