Protein Synthesis and Cellular Control

DNA, RNA, Protein Synthesis, Transcription & Translation, Body Plans, Mutation, Meiosis, Inheritance, Epistasis, Chi-squared, Variation, Genetic Drift, Hardy-Weinburg Principle and Speciation

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  • Created by: Eve
  • Created on: 30-05-10 13:59

DNA, RNA and Protein Synthesis

Genes are sections of DNA found on chromosomes.

Genes code for proteins - they contain the instructions to make them.

Proteins are made from amino acids. The order of bases in the gene determines the order of amino acids. Each amino acid is coded for by a sequence of 3 bases (a codon) in a gene.

Different sequences of bases code for different amino acids - this is the genetic code. Other codons are used to tell the cell when to start and stop production of a protein - start and stop codons.

DNA molecules are found in the nucleus of the cell, but ribosomes for protein synthesis are found in the cytoplasm.

DNA is too large to move out of the nucleus so a section is copied into RNA (transcription). The RNA leaves the nucleus and joins with a ribosome in the cytoplasm, where it can be used to synthesis a protein (translation).



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DNA, RNA and Protein Synthesis

Two types of RNA

1. mRNA:

  • Made in the nucleus
  • 3 adjacent bases called a codon
  • It carries the genetic code from the DNA in the nucleus to the cytoplasm where it is used to make a protein

2. tRNA:

  • Found in the cytoplasm
  • It has an amino acid binding site at one end and a sequence of 3 bases (anticodon) at the other end.
  • It carries amino acids to ribosomes during translation


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Transciption

1. RNA polymerase attaches to the DNA double-helix at the beginning of gene

2. The hydrogen bonds between the two DNA strands break and the DNA uncoils at that point

3. One of the strands is used as the template strand to make an mRNA copy

4. The RNA polymerase lines up free nucleotides which pair up and are joined together, forming an mRNA molecule

5. RNA polymerase moves along the DNA, separating the strands and assembling the mRNA strand

6. The hydrogen bonds between the strands of DNA re-form once the RNA polymerase has passed by and the strands coil back into a double helix.

7. When RNA polymerase reaches a stop codon, it stops making mRNA and detaches from the DNA

8. The mRNA moves out of the nucleus through a nuclear pore and attaches to a ribosome in the cytoplasm.

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Transcription

1. The mRNA attaches itself to a ribosome and tRNA molecules carry amino acids to the ribsome

2. A tRNA molecule, with an anticodon that's complementary to the first codon on the mRNA, attaches itself to the mRNA by complementary base pairing

3. A second tRNA attaches itself to the next codon

4. The 2 amino acids attached to the tRNA molecules are joined by a peptide bond. The first tRNA molecule moves away, leaving the amino acid behind

5. A third tRNA molecule binds to the next codon on the mRNA. Its amino acid binds to the first two and the second tRNA molecule moves away

6. This process continues, producing a chain of linked amino acids until there's a stop codon on the mRNA molecule

7. The protein moves away from the ribosome and translation is complete.

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Control of Protein Synthesis

Protein synthesis can be controlled at the genetic level by altering the rate of transcription of genes. Genetic control of prokaryotes involves operons. An operon is a section of DNA that contains structural genes, control elements and a regulatory gene.

Lac Operon:

E.Coli is a bacterium that respires glucose, but it can use lactose if glucose isn't available. The genes that produce the enzymes to respire lactose are found on the lac operon. It has 3 structural genes - lacZ, lacY and lacA which produce B-Galactosidase and lactose permease.

When lactose is not present... The regulatory gene lacl produces the lac repressor which binds to the operator site when there's no lactose present and blocks transcription.

When lactose is present... It binds to the repressor, changing the repressor's shape so that it can no longer bind to the operator site. RNA polymerase can now begin transcription of the structural genes.

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Body Plans

A body plan is the general structure of an organism that are arranged in a particular way. Proteins control the development of a body plan, these are coded for by genes called homeotic genes.

  • Homeotic genes have regions called homeobox sequences that code for a part of the protein called the homeodomain.
  • The homeodomain binds to specific sites on DNA, enabling the protein to work as a transcription factor
  • The proteins bind to DNA at the start of developmental genes, activating or repressing transcription and so altering the production of proteins involved in the development of the body plan.

Apoptosis (programmed cell death) is a normal part of development. Once triggered, the cell is broken down in a series of steps:

  • The cell produces enzymes that break down important cell components such as proteins in the cytoplasm.
  • As the cell's contents are broken down, it begins to shrink and breaks up into fragments
  • These fragments are engulfed by phagocytes and are digested.
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Protein Activation

Some proteins produced by protein synthesis have to be activated to work.

Protein activation is controlled by molecules e.g. hormones.

Some of these molecules work by binding to cell membranes and triggering the production of cyclic AMP.

cAMP then activates proteins inside the cell by altering their 3D structure which changes the active site of an enzyme making it more or less active. E,g, cAMP activates protein kinase A.

  • PKA is an enzyme of 4 subunits.
  • When cAMP isn't bound, the 4 units are bound and are inactive
  • When cAMP binds, it causes a change in the enzymes 3D structure, releasing the active subunits - pKA is now active
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Mutations

Any change to the base sequence of DNA is called a mutation.

  • Substitution - one base is swapped for another e.g. ATGCCT > ATTCCT
  • Deletion - one base is removed e.g. ATGCCT > ATCCT
  • Insertion - one base is added e.g. ATGCCT > ATGACCT
  • Duplication - one or more bases are repeated e.g. ATGCCT > ATGCCCCT
  • Inversion - a sequence of bases is reversed e.g. ATGCCT > ACCGTT

The order of bases determines the order of amino acids in a protein. If a mutation occurs in a gene, the primary structure of the protein it codes for could be altered.

This may change the final 3D shape of the protein so it doesn't work properly, e.g. active sites in enzymes may not form properly, meaning that substrates can't bind to them.

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The effects of mutations

Some mutations have a neutral effect on a proteins function. This may be because:

  • The mutation changes a base in a triplet, but the amino acid that the triplet codes for doesn't change. This happens because some amino acids are coded for by more than one triplet.
  • The mutation produces a triplet that codes for a different amino acid, but the amino acid is chemically similar to the original so functions like the original.
  • The mutated triplet codes for an amino acid not involved with the protein's function, e.g. one that's located far away from the enzymes active site, so the protein works as normal.

Mutations with beneficial effects have an advantageous effect on an organism. E.g. some bacterial enzymes break down certain antibiotics. Mutations in the genes that code for these enzymes could make them work on a wider range of antibiotics. This is beneficial to the bacteria because resistance helps them survive.

Mutations with harmful effects have a disadvantageous effect on an organism. e.g. CF can be caused by deletion of 3 bases in the gene that codes for the CFTR protein. The mutated protein folds incorrectly, so its broken down. This leads to excess mucus production, which affects the lungs of CF sufferers.

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Meiosis

Meiosis is the cell division that happens in the reproductive organs to produce gametes.

Cells that divide by meiosis are diploid to start with but the cells that are formed from meiosis are haploid - the chromosome number halves.

Cells formed by meiosis are all genetically different because each new cell ends up with a different combination of chromosomes.

Before meiosis, interphase happens - the cell's DNA unravels and replicates so there are two copies of each chromosome in each cell.

Each copy of the chromosome is called a chromatid and a pair are called sister chromatids - joined by a centromere.

After interphase, the cells enter meiosis where they divide twice - meiosis 1 and meiosis 2.


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Prophase 1: Chromosomes condense and supercoil. Homologous chromosomes pair up. Crossing over occurs. Spindle begins to form. The nuclear envelope breaks down.

Metaphase 1: The homologous pairs line up across the centre of the cell and attach to the spindle fibres by their centromeres.

Anaphase 1: The spindles contract, pulling the pairs apart - one chromosome goes to each end of the cell.

Telophase 1: A nuclear envelope forms around each group of chromosomes and the cytoplasm divides so there are now 2 haploid daughter cells.

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Meiosis - Genetic Differences

Meiosis creates genetic variation - it makes gametes that are genetically different in 3 ways:

1. Crossing over of chromatids: During prophase 1, homologous chromosomes pair up. In each pair, one chromosome is maternal and one paternal. They have the same genes but different versions of the genes called alleles. The non-sister chromatids twist around each other and parts swap over. The chromatids contain the same genes but now have a different combination of alleles. The crossing over means that each of the four daughter cells formed from meiosis contains chromatids with a different combination of alleles.

2. Independent assortment of chromosomes: During meiosis 1, different combinations of maternal and paternal chromosomes go into each cell. So each cell ends up with different combinations of alleles. If alleles are on the same chromosome they'll go into the same cell, so are inherited together - linkage.

3. Independent assortment of chromatids: During meiosis 2, different combinations of chromatids go into each daughter cell. So each cell ends up with a different combination of alleles.

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Inheritance

Individuals have two alleles of each gene. Gametes contain only one allele for each gene. When two gametes fuse together, the alleles they contain form the offspring's genotype. Genetic diagrams can be used to predict the genotypes and phenotypes of the offspring produced if two parents are crossed. Monohybrid inheritance is the inheritance of a single characteristic controlled by different alleles.

Some genes have co-dominant alleles - both alleles are expressed in the phenotype, neither one is recessive. E.g. Sickle cell anaemia. People who are homozygous for normal haemoglobin HnHn don't have it. People who are homozygous for sickle haemoglobin HsHs have sickle cell anaemia. People who are heterozygous HnHs have an in between phenotype, with some normal and some sickle haemoglobin. The alleles are codominant as they are both expressed.

Some characteristics are sex-linked. The genetic information for gender is carried on 2 sex chromosomes. A characteristic is said to be sex-linked when the allele that codes for it is located on a sex chromosome. The Y chromosome is smaller than the X and carries fewer genes, so most genes on the sex chromosomes are only carried on the X chromosome. As males only have one X chromosome, they often only have one allele for sex linked genes, so because they only have one copy they express the characteristic of the allele even if its recessive. This makes males more likely to show recessive phenotypes for genes that are sex linked.

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Phenotypic Ratios & Epistasis

The phenotypic ratio is the ratio of different phenotypes in offspring. Genetic diagrams allow you to predict the phenotypic ratios in F1 and F2 offspring.

Monohybrid cross (NN x nn) produces all heterozygous in F1 and 3:1 ratio in F2. Dihybrid cross (NNGG x nngg) produces all heterozygous in F1 and 9:3:3:1 in F2 Codominant cross (HnHn x HsHs) produces all heterozygous in F1 and 1:2:1 in F2

Many genes control the same characteristic - they interact to form the phenotype. This can be because the allele of one gene masks the expression of the alleles of other genes - this is called epistasis. E.g. flower pigment is controlled by two genes, but one can mask the expression of the other. Crosses involving epistatic genes don't result in expected phenotypic ratios.

A dihybrid cross involving a recessive epistatic allele - 9:3:4

A dihybrid cross involving a dominant epistatic allele - 12:3:1

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The Chi-Squared Test

The chi-squared test is a statistical test that's used to see if the results of an experiment support a theory. First, the theory is used to predict a result - this is the expected result. Then, the experiment is carried out and the actual result is recorded - this is the observed result. To see if the results support the theory you have to make a hypothesis called the null hypothesis. The null hypothesis is always that there's no significant difference between the observed and expected results, and if there is, this is just due to chance. The chi-squared test is then carried out and the outcome either supports or rejects the null hypothesis. The chi-squared test can be used in genetics to test theories about the inheritance and characteristics.

Chi squared is calculated using the formula: X2 = Sum of (O-E)2/E O = observed result E = expected result

To find out if there is no significant difference between your observed and expected results, you need to compare your X2 value to a critical value. The critical value is the value of X2 that corresponds to a 0.05 level of probability that the difference between observed and expected results is due to chance. If X2 value is smaller than the critical value, there is no significant difference between the observed and expected results - the null hypothesis is accepted.

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Variation

  • Variation is the differences that exist between individuals.
  • Every individual is unique, even clones show some variation
  • Variation can occur within species e.g. variation in wingspan and colour
  • Variation can also occur between a species e.g. the lightest species of bird is the hummingbird.

Continuous variation is when the individuals in a population vary within a range, there are no distinct categories. e.g. height and weight.

Discontinuous variation is when there are two or more distinct categories, each individual falls into only one of these categories, there are no intermediates. e.g. sex or blood group.

Variation can be influenced by your genes. Individuals of the same species have the same genes but different alleles, these make up its genotype. Difference is genotype result in variation in phenotype. E.g. Blood group - there are 3 blood group alleles which result in 4 different blood groups. Inherited characteristics that show continuous variation are usually influenced by many genes - these characteristics are said to be polygenic e.g. skin colour. Inherited characteristics that show discontinuous variation are usually influenced by only one gene, said to be monogenic.

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The Effect of the Environment on Variation

Variation can be caused by differences in the environment e.g. climate and food. Characteristics controlled by environmental factors can change over an organisms life. E.g. accents and piercings.

Genetic factors determine genotype and the characteristics an organism's born with, but environmental factors can influence how some characteristics develop. Most phenotypic variation is caused by the combination of genotype and environmental factors.Phenotypic variation influenced by both, usually shows continuous variation.

Examples;

  • Height of pea plants - pea plants come in tall and dwarf forms (discontinuous variation) which is determined by genotype. However, the exact height of the tall and dwarf plant varies (continuous variation) because of environmental factors (e.g. light intensity affects how tall a plant grows).
  • Human body mass - this is partly genetic but its also strongly influenced by environmental factors, like diet and exercise. Body mass varies within a range, so it's continuous variation.
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Evolution by Natural Selection

The complete range of alleles present in a population is called the gene pool. New alleles are generated by mutations in genes. How often an allele occurs in a population is the allele frequency. The frequency of an allele in a population changes over time - this is evolution.

  • Individuals within a population vary because they have different alleles
  • Predation, disease and competition create a struggle for survival
  • Because individuals vary, some are better adapted to selection pressure than others
  • Individuals that have an allele that increases their chance of survival is more likely to reproduce and pass on the beneficial allele.
  • So the next generation who inherit the allele are more likely to survive and pass on their genes so the frequency of the beneficial alle increases from generation to generation, this is natural selection.

Whether the environment is changing or stable affects which characteristic are selected fro by natural selection. When the environment isn't changing much, individuals with alleles towards the middle of the range are more likely to survive - stabilising selection. When there's change in the environment, individuals with alleles of an extreme type are more likely to survive - directional selection.

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Evolution by Genetic Drift

Evolution also occurs due to genetic drift - instead of environmental factors affecting which individuals survive, breed and pass on their alleles, chance dictates which alleles are passed on.

  • Individuals within a population show variation in their genotypes (A and B)
  • By chance, the allele for one genotype (B) is passed on more often than others
  • So the number of individuals with the allele increases
  • If by chance the same allele is passed on more often repeatedly, it can lead to evolution as the allele becomes more common in the population

Evolution by genetic drift usually has a greater effect in smaller populations where chance has a greater influence. In larger populations, chance factors tend to even out across the whole population.

Evolution by genetic drift also has a greater effect because there's a genetic bottleneck - e.g. when a large population suddenly becomes smaller because of a natural disaster.

Example - The mice in a large population are either black or grey. The coat colour doesn't affect their survival. A large flood hits the population and the only survivors are grey mice and one black mouse. Grey becomes the most common colour due to genetic drift.

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Hardy-Weinberg Principle

The Hardy-Weinberg Principle predicts that allele frequencies in a population won't change from one change to the next. But this prediction is only true under certain conditions - it has to be a large population where there's no immigration, emigration, mutations or natural selection. There also needs to be random mating - all possible genotypes can breed with all others.

The Hardy-Weinberg equation can be used to estimate the frequency of particular alleles and genotypes within populations. If the allele frequencies do change between generation in a large population then immigration, emigration, natural selection or mutation have happened.

Allele frequency - p+q=1 p = frequency of the dominant allele q = frequency of the recessive allele

Genotype frequency - p2 + 2pq + q2 = 1 p2 = frequency of homozygous dominant genotype 2pq = the frequency of the heterozygous genotype q2 = the frequency of the homozygous recessive genotype

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Artificial Selection

Artificial selection is when humans select individuals in a population breed together to get desirable traits. There are two examples:

1. Modern Dairy Cattle - Farmers select a female with a very high milk yield and a male whose mother had a very high milk yield and breed these two together. Then they select the offspring with the highest milk yields and breed them together. This is continued over several generations.

2. Bread Wheat - Bread wheat is the plant from which flour is produced for bread making. Wheat plants with high wheat yield are bred together. The offspring with the highest yields are then bred together. This is continued over several generations.

Similarities between A.S and N.S - both change the allele frequencies in the next generations - the beneficial characteristics become more common, both may make use of random mutations when they occur.

Differences between A.S and N.S - in N.S the organisms that reproduce are selected by the environment, but in artificial this is carried out by humans. A.S aims for a predetermined result, but in N.S the result is unpredictable. N.S makes the species better adapted to the environment but A.S makes them more useful for humans.

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Speciation

A species is a group of similar organisms that can reproduce to give fertile offspring. Speciation is the development of a new species. It occurs when populations of the same species become reproductively isolated - changes in allele frequencies cause changes in phenotype that mean they can no longer breed together to produce fertile offspring.

Geographical isolation happens when a physical barrier divides a population of a species. Conditions on either side of the barrier will be slightly different e.g. climate. Because of this, different characteristics will become more common due to natural selection. Allele frequencies will change and mutations will change which can lead to changes in phenotype frequencies. Eventually, individuals from different populations will have changed so much that they wont be able to reproduce with one another to produce fertile offspring.

Reproductive isolation occurs because the changes in the alleles and phenotypes of the two populations prevent them from successfully breeding together. These changes include; seasonal, mechanical and behavioural changes. This can be the result of random mutations within a population, preventing members of that population from breeding with other members of the species

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Classifying a Species

The traditional definition of a species is a group of similar organisms that can reproduce to give fertile offspring. This is the biological species concept. However, this causes problems because you can't always tell if different organisms can reproduce to give fertile offspring. E.g. they may be extinct, they may produce asexually or their may be practical or ethical issues involved.

Instead, scientists use the phylogenetic species concept to classify organisms. Phylogenetics is the study of the evolutionary history of groups of organisms.

All organisms have evolved from shared common ancestors. The more closely related two species are, the more recently their last common ancestor will be.

Phylogenetics tells us what is related to what and how closely related they are. Scientists can use phylogenetics to decide which species an organism belongs to or if its a new species - if it's closely related to members of another species then its probably the same species, but if its quite different to any known species its probably a new species.

There is also problems with classifying organisms using this concept - i.e there is no cut off to say how different two organism have to be to be different species. E.g. Humans and chimpanzees are different species but 94% of out DNA is the same.

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Comments

danni

copied straight out of the book but thanks

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