CAPE BIOLOGY UNIT 1 SPEEDRUN Water consists of two slightly positive H atoms covalently bonded to one slightly negative O atom. Due to this, it is a dipole molecule. Water is electrically neutral. Water molecules can easily bond with each other (cohesion) and can act as an excellent solvent. FUNCTIONS OF WATER - Temperature regulation – due to high specific heat capacity and ability to evaporate easily - Universal solvent – Tiny +ve and –ve charges easily attract other molecules or ions - Allows mass flow – H-bonds produce cohesion and surface tension - Reactivity – Used in hydrolysis reactions, e.g. during digestion - Assists buffers – Has a neutral pH Carbohydrates are organic molecules that contain carbon, hydrogen and oxygen. They consist of: Monosaccharides (1 unit): Written as CH2On -- e.g. C6H12O6 (glucose) or C5H10O5 (ribose) Disaccharides (2 units), e.g. maltose and lactose Polysaccharides (more than 2 units), e.g. starch, glyocogen, cellulose Alpha glucose: HOH HOH OHH HOH Beta glucose: OHH HOH OHH HOH CONDENSATION REACTIONS (e.g. SUCROSE) - When many molecules combine, a molecule of water is lost. This is called a condensation reaction. - Observe the linkage between alpha-glucose and beta-fructose to form a sucrose molecule. The molecule of water will be lost and the two molecules will be joined by the O-molecule, seen next. CONDENSATION REACTIONS (e.g. SUCROSE) This is called a glycosidic bond, which occurs between sugars. • Sucrose is used for transport instead of glucose because it is much more complex, more energy-efficient and not as reactive as glucose. • Sugars with disaccharide bonds are termed ‘non-reducing sugars’. HCl is needed to break the glycosidic bond. POLYSACCHARIDES Can consist of thousands of sugar monomers and glycosidic linkages. They may form long chains or compact spirals. They are mostly insoluble and must be hydrolysed before being absorbed by the digestive system. The main 3 examples are: 1. Starch 2. Glycogen 3. Cellulose STARCH • A high-energy polysaccharide consisting of amylose and amylopectin. • Amylose forms a chain of many alpha-glucose molecules linked by alpha 1,4 glycosidic bonds. • Amylopectin consists of similar 1,4 glycosidic bonds but also branches linked by alpha 1,6 glycosidic bonds. GLYCOGEN • Starch is found in plants. Glycogen is found in animals. • Glycogen consists of much more branches than amylopectin and is usually a larger molecule, thus acting as a powerful energy reserve. CELLULOSE • Cellulose comprises thousands of beta-glucose molecules linked by beta 1,4 glycosidic bonds. They form a linear structure called a fibre. • Due to the many H-linkages, their bonds are extremely strong. Cellulose is insoluble. • Each alternating beta glucose molecule is inverted 180 degrees. • The linear chains can be linked and ‘stacked’ by H bonds. TRIGLYCERIDES • Triglycerides consists of three fatty acids bonded to a glycerol. • They are insoluble and are hydrophobic (not water-attracted). • Contain a –COOH (carboxyl) group that reacts with –OH groups of glycerol to form an ester bond. TRIGLYCERIDES • The diagram above shows the condensation reactions. • In triglycerides, all the C atoms are bonded to H, which makes them yield more energy upon breakdown than carbs. AMINO ACIDS • Amino acids are monomers of polypeptides and proteins. • They are used for cellular growth and repair. They also form molecules such as enzymes and hormones. They consist of a central C-atom bonded to: • • • • An H atom An amino group (NH2) A carboxyl group (-COOH) A side-chain or residue (“R” group) AMINO ACIDS • There are 20 different amino acids. • They are differentiated by their R-groups. Some are very simple, e.g. glycine (with just an H-atom). • Others are quite complex with aromatic rings, e.g. tryptophan. AMINO ACIDS (peptide bonds) • During condensation reactions, peptide bonds form between the C of one amino acid and the N of the other. PROTEIN STRUCTURES Primary - Sequence of a chain of amino acids determined by a gene. Secondary - Amino acids are linked by weak H bonds between the H of the amino group and O in the carboxyl group. - Alpha helix or beta-pleated sheet. PROTEIN STRUCTURES Tertiary - Multiple linked secondary structures. Involves multiple bonds: H, ionic, disulphide, hydrophobic interactions - 3D shape. May have prosthetic groups, e.g. haem in haemoglobin Quaternary - Multiple secondary and tertiary structures. In haemoglobin, there are two alpha- and two beta-chains with haem groups attached. FIBROUS AND GLOBULAR PROTEINS Fibrous proteins - Are insoluble in water. - Consist of repeating amino acid sequences. - Usually have a structural role. - E.g. collagen, keratin, elastin Globular proteins - Are soluble in water - Specific shapes and sequences. - Partake in chemical reactions. - E.g. Enzymes, insulin, haemoglobin COLLAGEN - Is a fibrous protein. - Used for structural support. - Found in areas such as cartilage, bones and tendons. - Consists of 3 polypeptide chains that form a triple helix. - Held together by H bonds. - Forms cross-links to become fibres. FOOD TESTS Reducing and non-reducing sugar - Add Benedict’s solution to sample in water bath. - Brick-red precipitate forms if sugar is present. Green in trace amounts. - For non-reducing sugars, dilute HCl is needed to break glycosidic bond, before neutralizing with NaOH. Starch - Add iodine solution to sample. - Blue-black colour in presence of starch. FOOD TESTS Proteins - Add Biuret reagent to sample. - Purple or lilac colour if protein present. Emulsion test for lipids - Pour ethanol into sample. Lipids dissolve in ethanol. - Add water. Hydrophobic lipid molecules disassociate with solution, forming a milky white layer at top. - If cloudy emulsion present, then lipids are present. DIFFERENCES BETWEEN LIGHT AND ELECTRON MICROSCOPES ANIMAL CELLS - Cytoplasm – Site of chemical reactions. Keeps shape. Mitochondria – site of ATP production Plasma membrane – regulates entry and exit of materials. Nucleus – Stores genetic material and regulates organelle activity. Rough ER – Protein synthesis. Smooth ER – Lipid synthesis. Golgi body – Receives proteins from ER and transports them to cell membrane. Lysosomes – Contains enzymes. Centrioles – Prduces microtubules to pull chromosomes to ends of cell during cell division. NUCLEUS • The nucleus contains long molecules of DNA called chromosomes, made up of threads called chromatin. • The nucleus is surrounded by a pair of membranes known as nuclear envelope. • The nuclear envelope has tiny openings called nuclear pores, which allow movement of ATP and RNA. • The nucleolus contains ribosomal RNA or rRNA, which helps with protein synthesis. TRY LABELLING THEM YOURSELF! TRY LABELLING THEM YOURSELF! TRY LABELLING THEM YOURSELF! TRY LABELLING THEM YOURSELF! DIFFERENCES BETWEEN PLANT AND ANIMAL CELLS PROKARYOTIC CELLS - Have no nucleus, but contain a nucleoid region and plasmids (circular DNA). - Have small, 70S ribosomes. - No membrane-bound organelles, e.g. no mitochondria, chloroplasts, ER, etc. - Small. Usually between 5-10 µm. - Have cell walls made of peptidoglycan, e.g. bacteria. EUKARYOTIC CELLS - Have a nucleus. DNA in long helical strands connected to histones. - Have larger, 80S ribosomes. - Plant cells have cellulose cell walls. - Larger, as much as 100 µm. - Some have flagella, e.g. sperm. Many prokaryotes also have flagella, e.g. E. coli bacteria ENDOSYMBIOTIC THEORY - “Endosymbiotic” – One organism that lives within another organism, of which at least one organism benefits. - The theory states that mitochondria and chloroplasts in eukaryotic cells were once prokaryotes. - A large host prokaryote engulfed a mitochondria-like prokaryote and a chloroplast-like prokaryote and gained the ability to photosynthesise and yield ATP through respiration. EVIDENCE FOR ENDOSYMBIOTIC THEORY Mitochondria and chloroplasts: 1. Have their own circular DNA, like prokaryotes. 2. Have their own ribosomes, similar in size to those in prokaryotes. 3. Are similar in size to many prokaryotes. 4. Divide by binary fission, while eukaryotic cells divide by mitosis. 5. Inner membranes have prokaryotic structure, while outer has eukaryotic structure. TRANSVERSE SECTION OF A PLANT ROOT 1. 2. 3. 4. Epidermis – root hairs allow water absorption (large surface area) Cortex – Move water to the centre of root through cells or cell walls. Endodermis – Waterproof layer. Contains Casparian strips. Vascular bundle – Contains xylem and phloem for water and sucrose transport. TRANSVERSE SECTION OF A PLANT STEM Cambium – Responsible for secondary growth of stems. Sclerenchyma (dead) – Used for support. Collenchyma (alive) – Also support. PHOSPHOLIPIDS • Each phospholipid consists of a hydrophilic phosphate head and two hydrophobic fatty acid tails. They are amphipathic. • The head is bonded to the tails via a glycerol molecule. • They form phospholipid bilayers, which form cell membranes. THE FLUID MOSAIC MODEL The model shows a double layer of phospholipids, with the hydrophilic phosphate heads facing outward and hydrophobic fatty acid tails inward. Within this are intrinsic proteins (span the bilayer) and extrinsic proteins (do not span bilayer). Think of the model as “protein icebergs floating in a sea of phospholipids”. THE FLUID MOSAIC MODEL • Cholesterol is found between phospholipids to maintain fluidity of membrane. • Glycolipids and glycoproteins on the surface help with cell-to-cell signalling. • Water and polar molecules cannot diffuse through the phospholipids. PROTEIN CHANNELS AND CARRIERS • Protein channels allow facilitated diffusion of larger, polar molecules, e.g. glucose, RNA. • Specialized channels called aquaporins transport water. • Protein carriers bind specific molecules for transmembrane movement, e.g. ATP. SIMPLE AND FACILITATED DIFFUSION • Diffusion is the net movement of molecules from regions of higher to lower concentration. It does not require ATP. • Simple diffusion allows molecules (e.g. gases) to move in and out of the cell via the phospholipid bilayer. • Facilitated diffusion requires the use of transmembrane proteins. SIMPLE AND FACILITATED DIFFUSION • Simple diffusion allows a directly proportional relationship between substance concentration and diffusion rates. • Facilitated diffusion requires the use of protein channels, so the rate of diffusion plateaus if all of the channels are ‘in use’. ACTIVE TRANSPORT • Active transport moves molecules against a concentration gradient, using ATP. • An example of this occurring is when maintaining the balance K+ ions and Na+ ions in a cell. The K+ ions are pumped into the cell by the carrier protein as it changes shape, and Na+ ions are pumped out. ENDO- AND EXOCYTOSIS • Endocytosis moves substances in, absorbing them, e.g. engulfing pathogens. • Exocytosis moves substances out, releasing them from the cell, e.g. removing toxins from the cell cytosol. • Both methods of transport are used for bulk movement of materials. ATP is required to form vesicles (sacs), which form from or fuse with the cell membrane. OSMOSIS AND WATER POTENTIAL • Think of water potential (ψ) as the pressure that pushes water molecules across a membrane. • Hypotonic – high ψ, low solute conc. • Hypertonic – low ψ, high solute conc. • Water potential has a negative value. The more solute there is, the more negative ψ becomes. The highest ψ is for pure water, which is zero. HYPO- AND HYPERTONIC • In hypotonic solutions (higher ψ), water enters cell, causing it to swell and undergo lysis. Plant cells do not burst due to their cell walls. • In hypertonic solutions (lower ψ), water exits cell, causing it to shrivel (plasma membrane retracts in plant cells). • In isotonic solutions (same ψ), no net flow of water occurs. DETERMINING WATER POTENTIAL Place potato strips in different molarities of solute. If there is no change in length, there was no difference in water potential inside and outside of the cell (ψsolution = ψpotato). ENZYMES • Biological catalysts made of protein. They lower activation energy needed for reaction. • Globular proteins, tertiary structure, 3D shape. • Contains specific amino acid chains. • Contains a cleft called an ‘active site’ that a substrate would fit into. • May be anabolic (combine small molecules to larger). • Or catabolic, breakdown large molecules into smaller. ENZYME MODE OF ACTION • Enzymes bind substrate molecules to form an enzyme-substrate complex and convert them into products. • The enzyme is unaltered by the end. • It does this by fitting substrates into specific active sites (lock and key mechanism). • Sometimes the enzyme alters its shape slightly to accommodate substrate. This is called induced fit. RATE OF ENZYME REACTION • A – substrates rapidly bind to available enzyme. • B – all of the enzymes are currently ‘occupied’, so substrates must now ‘wait’ for an active site to be free. Rate of product formation decreases. • C – very few substrate molecules left, so product formation rate is very low. It plateaus when there is no more substrate left. INCREASING SUBSTRATE CONCENTRATION • Same as before, if there are limited enzymes, they become ‘occupied’ with substrate quickly. • Reaction rate slows down as substrates must ‘wait’ for active sites to be free. • Vm refers to how fast the enzyme can catalyze the reaction. INCREASING ENZYME CONCENTRATION • Think of increasing the amount of enzymes as adding more tellers to the bank. Customers can now access multiple tellers and transactions occur at a greater rate. • There are more enzymes that are able to interact with substrate. • Enzyme concentration increases the initial rate of reaction in a proportionate manner. ENZYME ACTIVITY VS TEMPERATURE • Kinetic energy in substrate molecules allows them to rapidly move and eventually bind with enzymes. • Low energy causing slow movement, making binding less likely. Rate of reaction initially increases with temperature. • Until an optimum temp (40oC) in graph. • In high temp, the tertiary protein structure of enzyme breaks down, H-bonds break and enzyme’s active site deforms (denaturation). ENZYME ACTIVITY VS pH • Think of pH as suppression of H ions. The lower the pH, the higher the number of H ions. • Differences in pH can break ionic bonds, change the tertiary structure of the enzyme protein, deform the active site and cause denaturation. • On the graph, pepsin has an optimum pH of 2.5 (acidic) and trypsin’s optimum pH is about 9 (alkaline). ENZYME INHIBITORS • Decrease the rate of an enzyme reaction. • They prevent or limit the binding of substrates to active sites of enzymes. • Inhibitors may be similarly shaped to substrates and bind to the active site instead (competitive inhibition). • They may bind to another attachment site (allosteric site) and disrupt the shape of the enzyme (non-competitive inhibition). COMPETITIVE AND NON-COMPETITIVE INHIBITION • Competitive – Inhibitor temporarily binds to active site, ‘blocking’ substrate from entering. Usually, a reversible process, so only slows down product formation. • Non-competitive – Inhibitor binds to allosteric site. Can be irreversible if it permanently alters 3D shape of enzyme and active site, stopping product formation altogether. COMPETITIVE AND NON-COMPETITIVE INHIBITION • Competitive – Think of it as someone taking too long in the toilet, preventing you from entering. You will eventually get in there, though. • Non-competitive – Someone has destroyed the toilet, preventing anybody else from using it! COMPETITIVE AND NON-COMPETITIVE INHIBITION • No inhibitor – Typical reaction rate. • With competitive inhibitor – Increasing substrate conc. can combat effects of inhibitor. Still attains the maximum velocity of reaction (Vm). • With non-competitive inhibitor – Substrate conc. has no effect. Maximum rate (Vm) is lower. Enzymes may be permanently STRUCTURE OF DNA • DNA has the shape of a double helix. • The strands are anti-parallel. • Each chain of the helix is made of nucleotides. • - DNA nucleotides consist of: Phosphate group Pentose sugar (deoxyribose) Nitrogenous base (adenine, cytosine, guanine, thymine) DNA BASES • A and G are purines (2 rings). • C and T are pyridimines (1 ring) • Bases form complementary pairs. - A binds to T (apple in tree) - C binds to G (car in garage) • One strand is marked 3’ to 5’, while the other is 5’ to 3’. These refer to the numbered carbon of the sugar. SUGAR-PHOSPHATE BACKBONE • The diagram shows the two strands running in opposite directions (anti-parallel). • Each nucleotide is bonded via condensation reactions. Phosphates of one nucleotide bond to the sugar of another. This forms a sugar-phosphate backbone. • These linkages are called phosphodiester bonds. DNA REPLICATION When mitosis (cell division) occurs, DNA replicates to produce two copies, one for each daughter cell. How does this happen? 1. DNA helicase ‘unzips’ DNA into two separate strands by breaking H bonds. 2. DNA polymerase pairs free nucleotides with the ones attached to the original strands. 3. H bonds form, linking the two, creating two new identical DNA molecules. DNA REPLICATION • Since there is one old strand (the original) and one new strand (the one built by DNA polymerase), it is called semiconservative replication. • Very few errors occur during this process. However, if one does occur, it may result in a mutation or cancer. DNA and RNA Differences • DNA is double-stranded • RNA is single-stranded. • DNA’s sugar is deoxyribose. • RNA’s sugar is ribose. • DNA has thymine (T). • RNA has uracil (U) instead of thymine. • DNA is found in the nucleus. • RNA is found in the nucleus and cytoplasm. DNA TO PROTEIN • A gene is a sequence of DNA that codes for a polypeptide or protein. • This occurs in the ribosomes in cytoplasm. • First, the DNA sequence must be ‘transcribed’ onto a messenger RNA (mRNA) strand. This is because mRNA is mobile and can exit the nucleus to go to ribosomes. • The mRNA sequence is read in 3-letter codons and ‘translated’ into amino acid seqences. TRANSCRIPTION • Production of an mRNA molecule with complementary base sequences to a DNA strand. • In RNA, thymine (T) is replaced with uracil (U), so A binds with U. • Example: TAC pairs with AUG. This is a triplet codon. TRANSCRIPTION • DNA helicase breaks H bonds, thus ‘unwinding’ DNA into two separate strands. • RNA polymerase allows free nucleotides to bind to the DNA strand to build the mRNA strand, which is in a 5’ to 3’ direction. • The mRNA elongates as more nucleotides keep linking. The mRNA exits the nucleus. TRANSLATION • Each triplet codon is linked to a particular amino acid. • Transfer RNA (or tRNA) in the cytoplasm each have a particular amino acid binded to them. • The ribosome ‘reads’ the mRNA sequence and tRNA pairs with the codon. Each tRNA has an anticodon that attaches to the codon (e.g. CGC on mRNA will pair with a GCG on tRNA). TRANSLATION • mRNA is read by ribosome. tRNA anticodons pair with complementary mRNA codons. • An amino acid is deposited. Peptide bonds form a polypeptide chain. • This polypeptide will then ‘fold’ into a 3D shape, a protein. DNA AND PHENOTYPE • DNA determines gene sequence and thus, amino acid sequence and proteins. • Phenotype is the physical expression of a gene, e.g. skin colour. • DNA can determine production of melanin proteins, which contribute to darker skin colour. • External factors, such as sunlight, can stimulate melanin production. CELL DIVISION • - Mitosis Daughter cells identical. 1 cell division. 2 daughter cells. Diploid (2n) chromosome no. • - Meiosis Daughter cells are varied. 2 cell divisions. 4 daughter cells. Haploid (n) chromosome no. IMPORTANCE OF MITOSIS 1. Asexual reproduction – one parent produces identical offspring rapidly, e.g. Amoeba, Hydra 2. Growth – e.g. a zygote’s cells keep dividing to form an embryo. Or meristems of plants. 3. Tissue repair – regenerates cells lost due to damage or age. 4. Immunity – When a foreign invader enters the body, lymphocytes multiply to produce antibodies. STAGES OF MITOSIS • INTERPHASE - DNA replication occurs here. - Nucleolus still intact. • PROPHASE - Chromatin condenses to form chromosomes. - Nucleolus disappears and nuclear membrane begins breakdown. - Microtubules and spindles begin to form at centrioles. STAGES OF MITOSIS • - METAPHASE Nuclear membrane broken down. Chromosomes align at equator. Centrioles on polar ends of cell. • ANAPHASE - Chromosomes break at centromeres. - Sister chromatids move to poles of cell. STAGES OF MITOSIS • TELOPHASE AND CYTOKINESIS - Chromatids at poles unwind to form chromatin threads. - Spindle fibres break down. - Nuclear membrane and nucleolus reform. - Cytoplasm divides and cell splits in two (cytokinesis). Two identical daughter cells are formed from one parent cell. STAGES OF MITOSIS • A stained root tip squash micrograph of onion (Allium) is shown. • Label: • Interphase, Prophase, Metaphase, Anaphase, Telophase. STAGES OF MITOSIS • A stained root tip squash micrograph of onion (Allium) is shown. . HOMOLOGOUS CHROMOSOMES • The figure to the right shows the visual appearance of all 23 pairs of human chromosomes. • The first 22 pairs are similar in shape and carry the same genes on the same positions (loci). These are homologous. • The 23rd pair are the sex chromosomes (X or Y). They do not have the same shape or loci. They are not homologous. DIPLOID AND HAPLOID • Diploid cells have the full set of chromosomes (46 in humans). These are usually every cell in the body (somatic cells) besides gametes. • Haploid cells have half the number of chromosomes (23 in humans). These are found in gametes. A NOTE ON CHROMOSOMES AND CHROMATIDS • When a chromosome is in its duplicated state, it has 2 chromatids (sister chromatids) but is still considered 1 chromosome. • When the chromatids separate (during anaphase), each unit is still referred to as a chromosome. • To make it less confusing, just count each unit and not each chromatid. MEIOSIS • Occurs in organisms that must produce gametes for sexual reproduction. • Forms 4 haploid daughter cells that are all genetically varied. This takes two cell divisions, named Meiosis I and Meiosis II. • When the chromosomes align, they pair up and DNA ‘crosses over’ or mixes. • These pairs are called bivalents. Where the loci cross are called chiasmata. MEIOSIS MEIOSIS I AND II Meiosis II’s events are very similar to Mitosis. Meiosis I - Instead of chromosomes aligning independently in equator, they pair up into bivalents. - The chromosome number is halved during Anaphase I. MEIOSIS AND GENETIC VARIATION • CROSSING OVER – During pairing up, they cross loci at chiasmata and swap DNA. • INDEPENDENT ASSORTMENT – When chromosomes pair up, one comes from the mother and one from the father. These pairs are independent of each other, resulting in a massive number of combinations. • RANDOM FERTILIZATION – Each gamete contains a random mix of DNA. The gametes that fuse with each other are up to chance. ADVANTAGES OF GENETIC VARIATION • SLOWING DISEASE SPREAD – Each member of a species can have varying levels of immunity or adaptation against communicable diseases. • ADAPTATION TO ENVIRONMENT CHANGES – Ensures some individuals are able to overcome selective pressures such as extremes in climate or temperature and continue the species. • LIMITING OVERCOMPETITION – Needs for survival such as diet and habitat would differ, thus preventing the need to fight for limited resources. E.g. The Galapagos Island finches. GENE MUTATIONS • A mutation is a random error during copying DNA, usually during DNA replication. There are three main types of gene mutations: • SUBSTITUTION - A single base is replaced by another. • DELETION – The loss of a base pair. • INSERTION – The addition of a base pair. FRAMESHIFT MUTATIONS • Deletion and addition are considered frameshift mutations. • Bases are ‘transcribed’ and ‘translated’ in triplet (3-letter) codons. • So, after deletion, the first codon TGG changes to GGC. The next codon, which is supposed to be CAG, would now begin with AG… • In addition, the first codon TGG changes to ATG. • This means the ribosomes may build entirely differently polypeptide sequences based on this error. SICKLE CELL ANAEMIA • Sickle cell anaemia is a disease where red blood cells have a sickle shape instead of their biconcave shape. This limits oxygen uptake and flexibility. They can also create blockages. • A single base pair has been substituted for another. • The incorrect triplet is transcribed onto the mRNA molecule. • A different amino acid is formed (VAL instead of GLU). • As a result, the haemoglobin protein structure and function changes. CHROMOSOME MUTATIONS • Chromosome mutations are changes in the cell’s chromosome number or structure. During meiosis, the chromosomes are unevenly pulled apart. • • • Down syndrome – an extra chromosome (47 chromosomes) Klinefelter’s syndrome – XXY chromosomes Turner syndrome – one X chromosome in women INHERITANCE COMMON TERMS AND DEFINITIONS • Gene – a nucleotide sequence which determines formation of a protein. • Allele – A variant of a gene. • Dominant – describes an allele that will express its trait if a different allele is present. • Recessive – describes an allele that will only express its trait if a dominant allele is absent • Codominance – Describes alleles that produce a combined effect when expressed together • Genotype – A gene combination that will express a trait (e.g. FF, Ff, ff) • Phenotype – The observable characteristics expressed by a gene. • Homozygous – A genotype where both alleles are the same (e.g. FF or ff) • Heterozygous – A genotype where both alleles are different. (e.g. Ff) MONOHYBRID INHERITANCE (Punnett Square) • Using Cystic Fibrosis (CF) as an example. It is inheritable. Causes the body to produce large amounts of thick mucus in the lungs. The mucus leads to bacterial overgrowth and infection. • CF is caused by a faulty allele ‘f’. The normal allele, ‘F’, is dominant. A patient suffering from CF will have the genotype ‘ff’. • How can two parents who don’t suffer from CF have a child with CF? MONOHYBRID INHERITANCE (Blood Types) • In inheritance of ABO blood type alleles, A and B are both codominant. If together, they will express the blood type AB. • The A and B alleles are dominant to the O alleles (which are recessive). • How can a Type A father and a Type B mother have a child with Type O? SEX-LINKED ALLELES • The Y chromosome has less available positions (loci) for alleles than the X chromosome. Some alleles cannot be present on the Y chromosome. • Haemophilia occurs due to the inheritance of a faulty ‘h’ allele on an X chromosome. • Since it cannot be inherited via a Y chromosome, a father cannot pass on a faulty allele to his son (since his son receives the Y chromosome from him) SEX-LINKED ALLELES • How can two parents who do not suffer from haemophilia have a child who suffers from haemophilia? DIHYBRID INHERITANCE • Occurs when TWO alleles are inherited at the same time. • Let’s look at traits of peas where: - Round (R) is dominant to wrinkled (r) - Yellow (Y) is dominant to green (y). DIHYBRID INHERITANCE DIHYBRID INHERITANCE (try one yourself!) DIHYBRID INHERITANCE (try one yourself!) EPISTASIS • Epistasis occurs if one pair of alleles directly influences the expression of another pair. • For example, imagine ‘B’ is black coat and ‘b’ is brown coat. • But ‘C’ represents melanin production and ‘c’ represents albino (no melanin). • Every mouse with ‘cc’ (albino) cannot have a brown or black coat, despite the ‘B’ or ‘b’ alleles. EPISTASIS (try it yourself!) B – Black, b – brown C – Melanin, c – albino Write in the genotypes of the mice in the boxes that match their colour coats. Then write the phenotypic ratio. EPISTASIS (try it yourself!) B – Black, b – brown C – Melanin, c – albino Remember: Any mouse with ‘cc’ cannot produce melanin, so will not have a black or brown coat. Phenotypic ratio: 9 black : 3 brown : 4 albino CHI-SQUARE TESTS • A chi-square test is a statistical test used to compare observed results with expected results for significant differences. • Sometimes external variables such as environmental factors, mutations or human intervention may be affecting an experiment. The chi-square test is used to determine if those variables exist. • To perform a statistical test, a null hypothesis (H0) is set up. It would read as: There is no significant difference between the observed and expected results. An alternative hypothesis (H1) would read the opposite: There is a significant difference between the observed and expected results. CHI-SQUARE TESTS CHI-SQUARE TESTS CHI-SQUARE TESTS CHI-SQUARE TESTS (example) • In the Punnett square to the right, 75% of peas are round and 25% are wrinkled. • Let’s say 7324 plants were observed. Out of that, 5474 had round peas and 1850 had wrinkled. Let’s now determine what was expected: Round = 75% x 7324 = 5493 Wrinkled = 25% x 7324 = 1831 CHI-SQUARE TESTS (example) • • • Next, determine the degrees of freedom (df). This is easy – just take the no. of phenotypes and minus one. In this case, there are 2 phenotypes, so there is 1 d.f. Now, determine the ‘p value’. We look at a critical value of 0.05. CHI-SQUARE TESTS (example) • • • • At 0.05, we can see the p value is 3.84. We now compare that value (3.84) to the chi-square value (0.263). Since our chi-square value is MUCH lower, we can accept the null hypothesis… …and conclude that there was no significant difference between our observed and expected results. CHI-SQUARE TESTS (2nd example) • • Try this one yourself! Complete the top row and Chi-square (X2) value. How many degrees of freedom would be there? (Remember d.f. = No. of phenotypes – 1) CHI-SQUARE TESTS (2nd example) • • These are your answers! There would be 3 degrees of freedom (4 phenotypes – 1). CHI-SQUARE TESTS (2nd example) • • Now look at the probability table. Remember the chi-square value was 5.8. With 3 d.f., what is the p value? CHI-SQUARE TESTS (2nd example) • • We look at the critical value (0.05) column at 3 d.f. The p value is 7.82. Our Chi-square value is 5.8. Is it a significant difference or not? CHI-SQUARE TESTS (2nd example) • • Chi square value of 5.8 is less than the critical value of 7.82… …therefore we accept the null hypothesis! (There is no significant difference between observed and expected results. GENETIC ENGINEERING • Definition: The altering of an organism’s DNA, either by inserting DNA from another species or changing the organism’s genome. • Altered DNA is called recombinant DNA. An organism with recombinant DNA is called a genetically modified organism, or GMO. • A common example are GloFish, which are zebrafish fused with bioluminescent jellyfish DNA. GENETIC ENGINEERING – how? 1. 2. 3. Make copies of the target DNA using an enzyme, reverse transcriptase and DNA polymerase. Restriction enzymes are like DNA scissors. They cut similar-shaped lengths of DNA from both human and the bacteria. DNA ligase is like DNA glue. It combines both segments of DNA. This is now recombinant DNA. 4. The recombinant DNA is then re-inserted into the bacteria, and the bacteria will now express that trait. GENETIC ENGINEERING – making multiple copies • • • • Reverse transcriptase allows mRNA to form DNA (the reverse of ‘transcription’). It builds one strand of DNA. This DNA copied from mRNA is called cDNA. DNA polymerase attaches free nucleotides to form the other strand. This process is called gene isolation. GENETIC ENGINEERING – cutting the DNA • As said, restriction enzymes are like DNA scissors. • Are used by bacteria to ‘cut’ viral DNA out of them, thus ‘restricting’ the virus from infecting them. • They cut specific base sequences of DNA, e.g. EcoRI cuts a GAATTC sequence (as well as its complementary DNA). • These are often asymmetrical and so leave “sticky ends”, which can easily form H bonds with complementary base pairs and be rejoined. GENETIC ENGINEERING – rejoining the DNA • DNA ligase is like DNA glue. • Both segments of cut DNA are mixed with the ligase enzyme. • It allows ‘sticky ends’ of cut DNA to join, linking the sugar-phosphate backbones of both cut segments. • When joined, the DNA is now called recombinant DNA. GENETIC ENGINEERING – inserting the recombinant DNA • The recombinant DNA plasmids are mixed in a solution containing bacterial culture. Some of the bacteria will take up the plasmid. • The new DNA (seen in red) is located in an area where there used to be a tetracycline-resistant gene. • We can expose all of the plasmids to tetracycline. The ones that die are the ones with that took up the target DNA. • By applying the same samples in plates without tetracycline, these colonies can be easily identified and isolated, and the desired product can be made in a fermenter. Let’s recap with insulin! 1. 2. 3. 4. Genes are isolated from human pancreatic beta cells and E. coli bacteria using reverse transcriptase. cDNA is formed. cDNA is cut with restriction enzymes to form sticky ends. DNA ligase rejoins the segments. H bonds form at sticky ends. Recombinant DNA is taken up by E. coli bacteria when mixed. The E. coli can now produce insulin. Recombinant bacteria is fermented with sugar and oxygen. Insulin is produced. GENE THERAPY • Gene therapy is the process of treating or preventing disease by altering the genes in a person’s cells. • We will use the example of Cystic Fibrosis treatment, caused by a defective allele that affects a protein called CFTR in the lungs. Because of this, mucus builds up. • The ‘repaired’ DNA is inserted into a virus and transported into the patient. GENE THERAPY – can it go wrong? • If the repaired DNA is delivered to the target cells to fix the CFTR protein, all is well for now. But… 1. 2. 3. 4. Viruses may mutate in patient. They may cause infection in immunocompromised patients. The repaired DNA may not be taken up by enough target cells, or any at all! White blood cells may destroy the viral vector before it reaches the target cells. GERMLINE VS. SOMATIC • Somatic gene therapy targets certain body cells (such as the CFTR proteins for CF). It has risks, but also many advantages. The altered DNA does not enter the gametes. • Germline gene therapy is very controversial. It allows gametes to pass on the recombinant DNA. Therefore, offspring will inherit this DNA and the entire gene pool can be altered as a result. ADVANTAGES and DISADVANTAGES • Environmental - Crops can produce their own pesticides. They can also be made frost-resistant. - If a GMO species of plant is able to pollinate with wild plants, it can cause an ecological and food web imbalance. - Golden Rice containing beta-carotene for Vitamin A helps those suffering from night blindness. ADVANTAGES and DISADVANTAGES • Ethical and Social - Can be seen as playing God. - The possibility of cloning humans raises social issues. - Producing designer babies for cosmetic desirable traits. - Production of biological weaponry is possible, especially if germline gene therapy technology is used. ADVANTAGES and DISADVANTAGES • Medical - Gene therapy is continuously being researched and improved to treat diseases such as CF, SCID and lymphoma. - CRISPR-Cas9 is a major scientific breakthrough in gene editing that can possibly treat even more diseases. - GMO’s may lead to diseases not yet known, due to viral mutations and allergens. - They may also reduce genetic diversity over time, giving rise to new diseases. NATURAL SELECTION • Natural selection occurs when offspring that are well-adapted to their environments can survive and reproduce. • They pass on those advantageous traits to offspring, which can also survive. A species has a better chance of survival if there is high genetic variation in its members. Example: Galapagos finches were able to adapt to many different diets due to their varied beak size, thus preventing competition with each other. NATURAL SELECTION • These finches grouped themselves together in niches, e.g. thick beaked seed-eaters, thin-beaked insect-eaters. • These characteristics were amplified as they reproduced. Eventually, the groups differed so much from each other that their members became new distinct species. • This is called speciation. SPECIES CONCEPTS • Biological species concept - Two members of the same species are able to interbreed and produce fertile offspring. - Cannot apply to organisms that reproduce asexually, e.g. Amoeba • Phylogenetic species concept - Organisms can be classified according to defining traits or morphology. - Can include all organisms. - But polymorphism makes it error-prone, e.g. peacocks and peahens. DARWIN’S DEDUCTIONS Observations: 1. Members of a species vary between each other. 2. All organisms produce excess offspring. 3. Population numbers remain fairly constant over long periods of time. Deductions: 1. If traits can be inherited, organisms pass them on to their offspring. 2. There is a struggle for existence among members of each species. 3. Members that are best adapted to their environment are the ones most likely to survive, reproduce and pass on their advantageous traits. ANTIBIOTIC RESISTANCE • Penicillin is an antibiotic that prevents formation of bacterial cell walls. • Some bacteria have mutated to produce an enzyme that inactivates penicillin. They have developed antibiotic resistance. • These resistant bacteria survive and reproduce, rapidly increasing the population of penicillin-resistant strains of bacteria. TYPES OF SELECTION • There are three types of selection: 1. 2. 3. Directional selection Stabilizing selection Disruptive selection DIRECTIONAL SELECTION • One variant that has an extreme form of the trait is selected over the average and other extreme. • Example: Peppered moths (Biston betularia). Black moths will survive in dark, sooty environments by camouflaging. White and grey moths will be more visible to predators. STABILIZING SELECTION • Only the variant of average form is selected. The extremes are selected against. • Example: Robins that lay eggs in fours have the highest chance of survival. Too few means lower chance of survival. Too many leads to overcompetition. DISRUPTIVE SELECTION • Both extremes of the trait are selected over the average form. • Example: Male Chinook salmon compete to fertilize eggs. Large fish are competitive fighters while smaller fish are more stealthy. The average-sized salmon has neither advantage. ISOLATION MECHANISMS • Isolation mechanisms are barriers that prevent members of a species from interacting. These barriers can be geographical, behavioural, mechanical, ecological or temporal. • When isolation occurs, various groups of the same species may be subjected to different selective pressures (e.g. predators, harsh climates) and would have to adapt in different ways. • No gene flow may occur between the splintered populations. • These populations change over time and speciation may occur. ISOLATION MECHANISMS • Geographical barrier – Two species are physically separated by a landmass. • Ecological barrier – Two species live in the same area but rarely or never meet. • Behavioural barrier – Two species have different courtship behaviours and will not mate. ISOLATION MECHANISMS • Mechanical barrier – Two species are physically incompatible, in terms of size, genitalia or gametes. • Temporal barrier – Two species live in the same area but experience different times of sexual maturity. ALLOPATRIC SPECIATION • Same as geographical isolation. • Species will form splinter groups due to a separation by a land mass, such as a mountain or ocean. • The presence of this land mass means that the groups will not meet and thus, will not mate. • On either side of the mountain, there may be different selective pressures, such as different coloured trees, terrain, predators. Each member must now adapt to these pressures. SYMPATRIC SPECIATION • Occurs when there is no geographical separation. • Example: A species of fruit fly in North America named R. pomonella usually fed and laid their eggs on hawthorn berries. However, after apples were introduced in the 1800’s, some began laying eggs in apples. These populations are becoming increasingly distinct from each other and will one day undergo speciation. REPRODUCTION IN FLOWERING PLANTS • Male gametes are formed within pollen, found in anthers, in stamens. • Female gametes are found within embryo sacs found inside of the ovule, in the ovary. • Pollination occurs when pollen from an anther is deposited onto the stigma. • Fertilization occurs when the male gametes from the pollen fuse with the female gametes in the ovule. MALE PARTS OF FLOWER • Pollen grains are formed from microsporangial cells within four pollen sacs in the anther. • Fibrous layer – Thickened cellulose walls. • Tapetum – Provides nutrition to developing grains in pollen sac. • Stomium – Point of dehiscence (splitting) to release pollen. • Pollen mother cell – Undergoes meiosis to form gamete nuclei. FORMATION OF POLLEN • Formation of pollen grains occur when a pollen mother cell undergoes meiosis. • A tetrad of haploid cells called microspores are formed. • These then undergo mitosis to form two types of nuclei within each. FORMATION OF POLLEN • Pollen grains contain: - Exine – Outer waterproof wall - Intine – Inner wall with enzymes - Generative nucleus – Undergoes mitosis to form two male gamete nuclei - Tube nucleus – Forms pollen tube to deliver gamete nuclei to embryo sac. FEMALE PARTS OF FLOWER • Egg cell – Becomes zygote after fertilization. Haploid cell. • Funicle – Stalk-like connection between ovule to ovary. • Integuments – Develop into seed coat. • Micropyle – Allows passage of pollen tube during fertilization. • Antipodal cells – Nourishes embryo sac. • Synergids – Directs pollen tube growth to egg cell. • Polar nuclei – Becomes endosperm nucleus after fertilization. FORMATION OF EMBRYO SAC • A diploid megaspore mother cell undergoes meiosis to produce a tetrad of haploid megaspores. • Only one is functional. • This undergoes mitosis until it forms an embryo sac of 8 haploid nuclei. FORMATION OF EMBRYO SAC • All of the 8 cells in the embryo sac are haploid (n). • - There are: 3 antipodal cells 2 synergids 2 polar nuclei 1 egg cell POLLINATION • Pollination is the transfer of pollen from anther to stigma. • This can be done by insects or wind. • Self-pollination occurs within the same flower or between two flowers of the same plant. • Cross-pollination occurs between two flowers of different plants. POLLINATION • Each pollen grain has two nuclei: generative and tube nucleus. • Generative nucleus divides by mitosis to form two haploid male gametes. • The tube nucleus uses digestive enzymes to elongate and grow down the style to the ovary. • The two male gametes follow the pollen tube to the embryo sac. DOUBLE FERTILIZATION • One male nucleus (n) fuses with the egg cell (n) to form the zygote (2n). This will eventually develop into an embryo. • One male nucleus (n) fuses with the polar nuclei (2n) to form the endosperm nucleus (3n). • This forms the endosperm, which provides nutrition for the developing embryo. POST-FERTILIZATION STRUCTURES • After fertilization occurs, many changes occur in the flower: - Egg cell – becomes a zygote and then an embryo. Ovary – becomes the fruit. Ovary wall – becomes the fruit pericarp, storing many sugars. Ovule – becomes a seed, still attached to parent plant. Integuments – becomes seed coat. Endosperm nucleus – becomes endosperm, which nourishes embryo. Petals – wither and fall off. EMBRYONIC DEVELOPMENT 1. Zygote undergoes mitosis. A terminal cell forms from a parent basal cell. 2. Mitosis continues. A ‘belt’ of terminal cells form called a suspensor. 3. The first terminal cell keeps dividing to form a globular embryo. Early root (radicle) and shoot (plumule) develops, as well as early leaves (cotyledons). OUTBREEDING MECHANISMS • These are characteristics that ensure cross-fertilization occurs in plants. • Ensures genetic variation and diversity of the species. Maintains vigour in species, and aids in speciation. • These include: 1. Self-incompatibility and sterility 2. Dioecious plants 3. Protandry and protogyny 4. Heterostyly OUTBREEDING MECHANISMS • Self-incompatibility ensures pollen of the same alleles of a plant do not germinate. • Example: S1S2 plant will not allow pollen grains of S1 and S2 alleles to sprout pollen tubes. Only those that are S3 and S4. • Male sterility ensures pollen grains are not produced or are not viable. OUTBREEDING MECHANISMS • Dioecious plants – have male and female flowers on separate plants, making self-pollination impossible. • Monoecious means the plant has both male and female flowers, making self-pollination possible. • Protandry – Stamens mature before stigmas. • Protogyny – Stigmas are receptive to pollen before stamens mature. OUTBREEDING MECHANISMS • Heterostyly – The various forms of the flowers makes it difficult for self-pollination to occur due to stigma and anther position. • It is difficult for pin flowers to self-pollinate due to the stigmas being higher than the anthers. PLANT ASEXUAL REPRODUCTION • No gametes are produced. No fertilization occurs and so, there is no genetic variation. • Can occur via budding or fragmentation. • Vegetative propagation can be done with cuttings, e.g. sugarcane. • Tissue culture can produce large numbers of clone plants from a single ex-plant tissue in sterile settings. ADVANTAGES AND DISADVANTAGES OF ASEXUAL REPRODUCTION SPERMATOGENESIS • Occurs in the lumens of the seminiferous tubules in the testes. • Large Sertoli cells nourish the cells and regulate the process. • Germinal epithelium gives rise to spermatogonia cells, which then become primary and secondary spermatocytes after mitosis and meiosis. • Spermatids are then formed, which grow a flagellum to become spermatozoa. FEMALE REPRODUCTIVE SYSTEM • A secondary oocyte (not ovum) is released during ovulation from ovaries. • If fertilization occurs, the zygote is implanted on endometrium. • The endometrium allows growth of structures that exchange materials between the foetal and maternal bloodstream during pregnancy. OOGENESIS • Before birth, oogonia divide to form primary oocytes. Meiosis begins but ‘arrests’. • At puberty, meiosis continues and produces a secondary oocyte (gamete) and a polar body. Meiosis stops again. • The polar body is not viable, so it degenerates. • Meiosis finishes upon fertilization to form the ovum and another polar body, which degenerates. OOGENESIS Structures called follicles are formed within the ovary, which gradually mature. When ovulation occurs, the follicle ruptures leaving behind a corpus luteum, which secretes progesterone, allowing the endometrium to thicken. COMPARING SPERMATOGENESIS AND OOGENESIS SPERM CELL STRUCTURE • Its role is to transport male genetic material to the female gamete. • Head – Contains nucleus, and acrosome loaded with hydrolytic enzymes to digest a path into female gamete. • Neck – Contains centrioles that help form flagellum. • Body – Contains mitochondria that provide ATP for motility. • Flagellum – Comprises microtubules that allow movement in whip-like motions. SECONDARY OOCYTE STRUCTURE • Its role is to accept genetic material from the sperm cell during fertilization. • It is significantly larger than spermatozoa. They are non-motile. • Its nucleus contains half of the maternal DNA (the other half is in the polar body). • Much more cytoplasm than sperm cells. Has food storage (lipids) and many mitochondria. • Its plasma membrane has microvilli, which assist in attaching incoming sperm. COMPARING SPERMATOZOA AND SECONDARY OOCYTES FERTILIZATION OF OOCYTE • The fusion of male and female gamete nuclei. Takes place in the oviduct. • Uterine enzymes digest sperm cell plasma membranes. Sperm become capacitated, allowing them to swim faster towards egg. • Upon contact with zona pellucida, an impermeable fertilization membrane forms, preventing entry of other sperm. • Meiosis completes in oocyte, forming ovum and second polar body. IMPLANTATION • Zygote divides by mitosis to form a blastocyst. • Blastocyst moves from oviduct to endometrium, where it is implanted. • Trophoblast cells on blastocyst surface secrete enzymes to digest a ‘pocket’ in the endometrium. • Trophoblast cells undergo mitosis and specialize into chorionic villi, which connect foetal and maternal bloodstreams (the placenta). PLACENTAL FUNCTIONS • Gas exchange – Chorionic villi help oxygen flow from maternal to foetal blood in intervillous spaces. • Nutrient and antibody intake – Chorion facilitates diffusion of glucose and amino acids. • Waste transfer – Allantois allows removal of waste from foetal kidneys. • Blood pressure regulation – Reduces maternal blood pressure. AMNION FUNCTIONS • Shock absorber – Protects foetus from external injury. • Temperature regulator – Amniotic fluid absorbs excess heat, has high specific heat capacity. • Limb development – Movement in fluid facilitates limb growth and development. • Support – Fluid keeps foetus supported against gravity. • Blood barrier – Prevents intermingling of foetal and maternal blood and pathogens. HORMONAL REGULATION • GnRH – Stimulates release of LH and FSH. Secreted by hypothalamus. PITUITARY HORMONES (Gonadotropins) • FSH – Stimulates growth of eggs; regulates sperm production. • LH – Stimulates ovulation; release of gonadal hormones. GONADAL HORMONES • Oestrogen – Stimulates LH production; endometrium thickness. • Progesterone – Maintains endometrium thickness. • Testosterone – Stimulates sperm production. • Inhibin – Inhibits release of GnRH, and thus FSH and LH. GAMETOGENESIS HORMONES • GnRH released from hypothalamus. Stimulates release of FSH and LH. • LH binds to Leydig cells to secrete testerone. FSH binds to Sertoli cells, making them more receptive to testosterone. • FSH and testosterone both inhibit the release of GnRH, FSH and LH. Prevents testosterone levels from rising too high. OOGENESIS HORMONES • GnRH released from hypothalamus. Stimulates release of FSH and LH. • LH and FSH develop ovarian follicle, stimulating release of oestrogen and progesterone. • Oestrogen and progesterone inhibit GnRH, LH and FSH. • But when ovulation occurs, they allow increased secretion of GnRH, FSH and LH to allow follicle to rupture and release secondary oocyte. MENSTRUAL CYCLE • Follicular phase – FSH and LH triggers release of oestrogen from ovarian follicle, causing a surge in LH. • Ovulation – The LH surge triggers ovulation, causing secondary oocyte to be released from follicle. Follicle becomes a corpus luteum. • Luteal phase – Corpus luteum secretes progesterone to maintain endometrium thickness for implantation. OOGENESIS HORMONES • Menses – If no implantation occurs, progesterone levels drop and uterine lining sheds. This drop causes a slight increase in FSH and LH. • If a woman does become pregnant, the endometrium remains thickened. This is because the blastocyst secretes hCG, a hormone that ensures menses does not take place. • Only pregnant women produce hCG. BIRTH CONTROL • Birth control methods prevent pregnancy. They can be: - Contraception – prevention of fertilization - Anti-implantation – fertilization occurs, but not implantation of fertilized egg • - Contraceptive methods include: Barriers, e.g. condoms and diaphragms Sterilization, e.g. vasectomy or tubal ligation Oral contraceptives, which suppress ovulation Depo-Provera injections, which inhibit ovulation. • Anti-implantation methods include: - Morning after pill, which changes endometrium to limit implantation. - IUD’s, which stimulate immune responses to attack sperm. PRE-NATAL CARE • These are behaviours that a mother adopts to reduce ill health of foetus. - Proper diet – Folic acid to prevent spina bifida; iron for formation of haemoglobin; calcium for bones; avoiding foods that are unpasteurized. - Avoiding alcohol – May lead to reduced development, cleft palate and foetal alcohol syndrome (FAS). - Avoiding smoking – Nicotine constricts foetal blood vessels. Carbon monoxide and tar limit oxygen intake by build-up of mucus and destroying alveoli. - Rubella vaccine – Rubella can be fatal to foetuses. - Monitoring programs – Ultrasound probes monitor foetal heat rate and organ development.