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click here for freelancing tutoring sitesHierarchal structure of Proteins.

The primary structure of a protein is the linear arrangement, or sequence, of amino acid residues that constitute the polypeptidechain.Secondary structure refers to the localized organization of parts of a polypeptide chain, which can assume several different spatial arrangements. Without any stabilizing interactions, a polypeptide assumes a random-coil structure. However, when stabilizing hydrogen bonds form between certain residues, the backbone folds periodically into one of two geometric arrangements: an α helix, which is a spiral, rodlike structure, or a β sheet, a planar structure composed of alignments of two or more β strands, which are relatively short, fully extended segments of the backbone. Tertiary structure, the next-higher level of structure, refers to the overall conformation of a polypeptide chain, that is, the three-dimensional arrangement of all the amino acids residues. In contrast to secondary structure, which is stabilized by hydrogen bonds, tertiary structure is stabilized by hydrophobic interactions between the nonpolar side chains and, in some proteins, by disulfide bonds. These stabilizing forces hold the α helices, β strands, turns, and random coils in a compact internal scaffold. Thus, a protein’s size and shape is dependent not only on its sequence but also on the number, size, and arrangement of its secondary structures. For proteins that consist of a single polypeptide chain, monomeric proteins, tertiary structure is the highest level of organization.Multimeric proteins contain two or more polypeptide chains, or subunits, held together by noncovalent bonds. Quaternary structuredescribes the number (stoichiometry) and relative positions of the subunits in a multimeric protein.

In a fashion similar to the hierarchy of structures that make up a protein, proteins themselves are part of a hierarchy of cellular structures. Proteins can associate into larger structures termed macromolecular assemblies. Examples of such macromolecular assemblies include the protein coat of a virus, a bundle of actin filaments, the nuclear pore complex, and other large submicroscopic objects. Macromolecular assemblies in turn combine with other cell biopolymers like lipids, carbohydrates, and nucleic acids to form complex cell organelles.

Movement through Plasma MembraneDiffusionOne method of movement through the membrane is diffusion. Diffusion is the movement of molecules from a region of higher concentration to one of lower concentration. This movement occurs because the molecules are constantly colliding with one another. The net movement of the molecules is away from the region of high concentration to the region of low concentration.Diffusion is a random movement of molecules down the pathway called theconcentration gradient. Molecules are said to move down the concentration gradient because they move from a region of higher concentration to a region of lower concentration. A drop of dye placed in a beaker of water illustrates diffusion as the dye molecules spread out and color the water.

OsmosisAnother method of movement across the membrane is osmosis. Osmosis is the movement of water from a region of higher concentration to one of lower concentration. Osmosis often occurs across a membrane that is semipermeable. A semipermeable membrane lets only certain molecules pass through while keeping other molecules out. Osmosis is really a type of diffusion involving only water molecules.

Facilitated diffusionA third mechanism for movement across the plasma membrane is facilitated diffusion. Certain proteins in the membrane assist facilitated diffusion by permitting only certain molecules to pass across the membrane. The proteins encourage movement in the direction that diffusion would normally take place, from a region with a higher concentration of molecules to a region of lower concentration.

Active transportA fourth method for movement across the membrane is active transport. When active transport is taking place, a protein moves a certain material across the membrane from a region of lower concentration to a region of higher concentration. Because this movement is happening against the concentration gradient, the cell must expend energy that is usually derived from a substance called adenosine triphosphate or ATP. An example of active transport occurs in human nerve cells. Here, sodium ions are constantly transported out of the cell into the external fluid bathing the cell, a region of high concentration of sodium. (This transport of sodium sets up the nerve cell for the impulse that will occur within it later.

EndocytosisThe final mechanism for movement across the plasma membrane is endocytosis, a process in which a small patch of plasma membrane encloses particles or tiny volumes of fluid that are at or near the cell surface. The membrane enclosure then sinks into the cytoplasm and pinches off from the membrane, forming a vesicle that moves into the cytoplasm. When the vesicle contains particulate matter, the process is called phagocytosis. When the vesicle contains droplets of fluid, the process is called pinocytosis. Along with the other mechanisms for transport across the plasma membrane, endocytosis ensures that the internal cellular environment will be able to exchange materials with the external environment and that the cell will continue to thrive and function.

Exocytosis:

 bulk movement of substances out of a cell by a vesicle merged with the cell membrane andexpelling its contents

Fluid-mosaic model of a plasma membrane: A model conceived by S.J. Singer and Garth Nicolson in 1972 to describe the structural features ofbiological membranes.

SupplementThe plasma membrane is described to be fluid because of its hydrophobic integral components such aslipids and membrane proteins that move laterally or sideways throughout the membrane. That means the membrane is not solid, but more like a 'fluid'.The membrane is depicted as mosaic because like a mosaic that is made up of many different parts theplasma membrane is composed of different kinds of macromolecules, such as integral proteins, peripheral proteins, glycoproteins, phospholipids, glycolipids, and in some cases cholesterol, lipoproteins.According to the model, the plasma membrane is a lipid bilayer (interspersed with proteins). It is so because of its phospholipid component that can fold in itself creating a double layer - or bilayer - when placed in a polar surrounding, like water. This structural feature of the membrane is essential to its functions, such as cellular transport and cell recognition.

The role played by organelles including ribosomes, endoplasmic reticulum, Golgi apparatus and associatedvesicles in the export of proteins. Below is the process of protein synthesis and export in eukaryotic cells:Transcription: DNA in the nucleus is transcribed into messenger RNA (mRNA) and then transported to thecytoplasm.2.Translation: mRNA is translated into a polypeptide chain (protein with itsprimary structure) by theribosomes, using amino acids carried by specific transfer RNA (tRNA). As the polypeptide chain is beingsynthesised it begins to form itssecondary structure.The mRNA code is read three nucleotides (acodon) at a time;anticodons on tRNA match specific codons on mRNA so that the correct amino acid is added to the polypeptide chain.3. Once the polypeptide chain is synthesised it moves into therough endoplasmic reticulum(ER), which transports it to the Golgi apparatus viavesicles.In theGolgi apparatusthe polypeptide chain undergoes further folding into a three-dimensional structure to form itstertiary and sometimes quaternary structure. The resultant proteins are then sorted and packaged into vesicles for transport to their next destinations, e.g.secreted from the cell by exocytosis.

Biology SAC 2: DNA Manipulation Tools and TechniquesMolecular GeneticsNature of genomes: A genome of an organism is its complete set of genetic instructions, encoded in DNA. For humans – consists of DNA of haploid set of autosomes, plus sex chromosomes. We have two genomes each, one copy of our genome from each of our parents. Sperm cell has one copy of a genome, and egg cells only have one copy. Both cells join together to make a cell containing two genomes, and the fertilized egg then has a complete set of instructions to make a new person. Genomes are made of a chemical called DNA. Nature of genes: A gene is a length of DNA that contains genetic instructions that we inherit from our parents, to make a chemical in your body. The genes are nucleotide sequences (A, G, T, C). The DNA in a gene usually codes for a protein, and a strand of DNA runs from 5 prime to 3 prime. They control various structures and functions in our body. Location of genes – on chromosomes that are found in the nucleus of a eukaryotic cell. Position on chromosome occupied by a gene is its locus. Average human chromosome carries a large number of genes that are arranged in a particular linear order. Larger chromosome = more genes carried.

Gene expression: Gene expression is the process by which genetic instructions are used to synthesize gene products. These products are usually proteins, which go on to perform essential functions as enzymes, hormones and receptors, for example. Genes that do not code for proteins such as ribosomal RNA or transfer RNA code for functional RNA products. Nature of the genetic code:The genetic information in the mRNA is composed of an alternating sequence of the four bases adenine (A), guanine (G), cytosine (C) and uracil (U). This alternating sequence provides the unique code specifying each of the 20 amino acids naturally found in protein. In the genetic code each of the 20 amino acids is represented by at least one codon. The genetic code is read by transfer RNAs (tRNA). Each tRNA has an anticodon that is complementary to the codon in the mRNA.

Role of RNA in Transcription: Transcription is the process of making an RNA strand from a DNA template, and the RNA molecule that is made is called the transcript. DNA maintains genetic info in the nucleus, RNA take that info into the cytoplasm where the cell uses it to construct specific proteins, RNA synthesis is transcription, protein synthesis is translation. RNA is single stranded, unlike DNA which is double stranded. It contains Uracil instead of Thymine and ribose instead of deoxyribose. Messenger RNA transmits information in a gene to cellular structures that build proteins. Each three mRNA bases in a row forms a codon that specifies a particular amino acid. Ribosomal RNA and proteins form ribosomes, which physically support the other participants in protein synthesis and help catalyze formation of bonds between amino acids. RNA processing in eukaryotes: RNA is often altered before it is active. Messenger RNA gains a cap of modified nucleotides and a poly A tail. Introns are transcribed and cut out, and exons are reattached by ribozymes. In eukaryotes, the nascent RNA is called primary transcript-RNA – needs to be processed and transported to the cytoplasm for translation to occur.• The processing steps are:– Addition of a 5’ 7-methyl guanosine cap (capping).– Addition of a poly-A tail at the 3’ end (polyadenylation)– RNA splicing to remove intervening sequences (remove introns).Eukaryotic RNA Processing: Capping• When the RNA chain is about 30 nucleotides long, the 5’ ends are modified by the addition of a guanine group in the opposite orientation:– involves a 5’-5’ triphosphate linkage.– Happens before transcription is finished = co-transcriptionally• They protect the growing RNA chain from degradation by nucleases. Eukaryotic RNA Processing: Polyadenylation• nascent RNA is cleaved downstream from the AAUAAA conserved sequence. – By ribonuclease• The enzyme poly(A) polymerase adds adenine ribonucleotides – up to 200 bases long at the 3’ end of the RNA.• The poly(A) tail– enhances the stability of eukaryotic mRNA and– regulates its transport to the cytoplasmic compartment.Eukaryotic RNA Processing: RNA splicing(RNA is called hnRNA - Heteronuclear RNA before splicing occurs)• Splicing is The mechanism by which introns are removed.• Introns are intervening sequences - not expressed in proteins• Exons are retained in the mature mRNA molecules.– expressing sequences

RNA Translation:In protein synthesis, three types of RNA participate and play different roles:

- Messenger RNA (mRNA): carries genetic information from DNA and is used as a template for protein synthesis.

- Ribosomal RNA (rRNA): major part of ribosomes where protein synthesis takes place. - Transfer RNA (tRNA): incorporates a particular amino acid subunit into the growing protein wen it

recognizes a specific group of three adjacent bases in the mRNA.

DNA Tools and Techniques: Gel Electrophoresis: used as a methods of visualizing DNA, and involves agarose gel. Agarose gel lets DNA move through it, but bigger pieces of DNA get trapped in the gel which makes them move more slowly. DNA has a negative charge which applies a current to the agarose gel and allows the DNA to move towards the positive end. A control called the standard is run in the first lane of every gel, and it contains a number of DNA fragments. PCR: Polymerase Chain Reaction – capable of producing enormous amplification (identical copies) of a short DNA sequence. DNA Sequencing:involves determining the sequence of nucleotides making up a length of DNA.- Restriction enzymes digest the strands and fragments re isolated by G.E.- The sequence is determined by;Denaturing DNA so it is single stranded, then using it as a template for DNA polymerase to resynthesis OR By chemicals analysis of the fragments.PLASMIDS are small circular DNA molecules found in many bacteria. Plasmids are self-replicating.RECOMBINANT DNA AND GENE CLONING: A DNA molecule make in vitro with segments from different organism is known as RECOMBINANT DNA.The same restriction enzymes are also used to cut open plasmids to ensure the same complementary sticky ends exist on the DNA fragments.RECOMBINANT PLASMIDS are those plasmids which took up the human gene (Are mixed with bacterial cells). Bacteria are made competent and plasmids can cross cell membranes and enter cells. DNA PROFILLING FROM DNA FINGERPRINTINGAdvantage over DNA fingerprinting:-Is far more sensitive and requires smaller quantities of DNA-Fragments differing in size by just one base pair can be distinguished-It uses several single-locus probes-much quicker to perform

GENE CLONING:Molecular cloning is used to assemble recombinant DNAmolecules and to direct their replication within host organisms. The method involves the replication of a single DNA molecule starting from a single living cell to generate a large population of cells containing identical DNA molecules. STEPS:(1) Choice of host organism and cloning vector, (2) Preparation of vector DNA, (3) Preparation of DNA to be cloned, (4) Creation of recombinant DNA, (5) Introduction of recombinant DNA into host organism, (6) Selection of organisms containing recombinant DNA, (7) Screening for clones with desired DNA inserts and biological properties.

Gene Delivery: A normal gene is inserted into the genome to replace an abnormal disease causing gene.

Biology SAC 3 RevisionPhotosynthesis:

Process of converting light energy into chemical energy where it is stored as glucose.

Process takes place in chloroplasts, more specifically chlorophyll – green pigment

Parts include upper and lower epidermis, stomates, vascular bundles (veins), and the mesophyll.

Upper and lower epidermis serve primarily as protection for the leaf. Stomates are holes which occur in the lower epidermis and are for air exchange (O2 and CO2) Vascular bundles (veins) are part of the plant’s transportation system, moving water and nutrients

around the plant as needed. Mesophyll cells contain chloroplasts and this is where photosynthesis occurs. Chlorophyll appears green because it absorbs red and blue light, and reflects green and yellow light.

The energy absorbed from the red and blue light is the energy that can be used for photosynthesis. Chemical reaction equation: 6CO2 + 6H2O (+ light energy) → C6H12O6 + 6O2. Involves the synthesis of organic compounds, hence endergonic reaction. Occurs in two stages:

- Light dependent stage: splitting of water - Dark Stage (light independent): production of carbohydrate.

CO2 undergoes reduction reaction to produce carbohydrate. Raw materials enter leaf via:

- Water from roots (xylem vessels) - CO2 via stomata (bi-products of cellular respiration)

Products leave the leaf: - Oxygen via stomata (or used in cellular respiration) - Glucose metabolized into other biomolecules stored as starch.

Cellular Respiration: Animals and organisms obtain the energy available in carbohydrates through the process of cellular

respiration. Through a complex series of metabolic processes, cells break down the carbohydrates and release the

energy. This energy is generally not needed immediately; it is mainly used to combine ADP (Adenosine Diphosphate) with phosphate ions to form ATP (Adenosine Triphosphate) molecules. The ATP can then be used for processes in the cells that require energy.

Cellular Respiration – three main stages. Glycolysis, Krebs Cycle, and Electron Transport. Glycolysis: literally means "splitting sugars." Glucose, a six carbon sugar, is split into two molecules of

a three carbon sugar. Input is 2 ATP molecules and 2NAD+ molecules. In the process, Output are two (or 4) molecules of ATP, two molecules of pyruvic acid and two "high energy" electron carrying molecules of NADH are produced. Glycolysis can occur with or without oxygen. In the presence of

oxygen, glycolysis is the first stage of cellular respiration. Without oxygen, glycolysis allows cells to make small amounts of ATP. This process is called fermentation.

Krebs Cycle: begins after the two molecules of the three carbon sugar produced in glycolysis are converted to a slightly different compound (acetyl CoA). Input: 2 pyruvate, 4 NAD, 1 CoA, 1 FAD, 1 ADP. It outputs 4 NADH, 4 H+, 3 CO2 , 1 ATP and 1 FADH2. .

Nicotinamide adenine dinucleotide (NAD) Flavin adenine dinucleotide (FAD) The Krebs Cycle occurs only when oxygen is present but it doesn't use oxygen directly. Electron Transport: requires oxygen directly. The electron transport "chain" is a series of electron

carriers in the membrane of the mitochondria in eukaryotic cells. Through a series of reactions, the "high energy" electrons are passed to oxygen. In the process, a gradient is formed, and ultimately ATP is produced.

Biology SAC 4.1.1

Cell Reproduction: Binary fission in prokaryotes:form of asexual reproduction and cell division used by all prokaryotes (bacteria). Single DNA molecule replicates and original cell is divided into two identical cells. Both copies attach to cell membrane, and it begins to grow between the two DNA molecules, then a cell wall forms between them which divides the original cell into two identical daughter cells. DNA Replication: 1)The first major step for the DNA Replication to take place is the breaking of hydrogen bonds between bases of the two antiparallel strands. The unwounding of the two strands is the starting point. The splitting happens in places of the chains which are rich in A-T. That is because there are only two bonds between Adenine and Thymine (there are three hydrogen bonds between Cytosine and Guanine). Helicase is the enzyme that splits the two strands. The initiation point where the splitting starts is called "origin of replication".The structure that is created is known as "Replication Fork".

2)One of the most important steps of DNA Replication is the binding of RNA Primase in the the initiation point of the 3'-5' parent chain. RNA Primase can attract RNA nucleotides which bind to the DNA nucleotides of the 3'-5' strand due to the hydrogen bonds between the bases. RNA nucleotides are the primers (starters) for the binding of DNA nucleotides.3)The elongation process is different for the 5'-3' and 3'-5' template. a)5'-3' Template: The 3'-5' proceeding daughter strand -that uses a 5'-3' template- is called leading strand because DNA Polymerase ä can "read" the template and continuously adds nucleotides (complementary to the nucleotides of the template, for example Adenine opposite to Thymine etc).

b)3'-5'Template: The 3'-5' template cannot be "read" by DNA Polymerase ä. The replication of this template is complicated and the new strand is called lagging strand. In the lagging strand the RNA Primase adds more RNA Primers. DNA polymerase å reads the template and lengthens the bursts. The gap between two RNA primers is called "Okazaki Fragments". 

The RNA Primers are necessary for DNA Polymerase å to bind Nucleotides to the 3' end of them. The daughter strand is elongated with the binding of more DNA nucleotides.4)In the lagging strand the DNA Pol I -exonuclease- reads the fragments and removes the RNA Primers. The gaps are closed with the action of DNA Polymerase (adds complementary nucleotides to the gaps) and DNA Ligase (adds phosphate in the remaining gaps of the phosphate - sugar backbone). Each new double helix is consisted of one old and one new chain. This is what we call semiconservative replication. 6

5)The lastthe TerminationPolymerase reaches to an end of the strands. We can easily understand that in the last section of the lagging strand, when the RNA primer is removed, it is not possible for the DNA Polymerase to seal the gap (because there is no primer). So, the end of the parental strand where the last primer binds isn't replicated. These ends of linear (chromosomal) DNA consists of noncoding DNA that contains repeat sequences and are called telomeresremoved in every cycle of DNA Replication.6)The DNA Replication is not completed before a mechanism of repairduring the replication. Enzymes likethe wrong nucleotides and the DNA Polymerase fills the gaps.Mitosis:daughter cells. Chromosomes do not pair up at equator. Diploid 2n (46).

The RNA Primers are necessary for DNA Polymerase å to bind Nucleotides to the 3' end of them. The daughter strand is elongated with the binding of more DNA nucleotides.4)In the lagging strand the DNA Pol I -exonuclease- reads the fragments and removes the RNA Primers. The gaps are closed with the action of DNA Polymerase (adds complementary nucleotides to the gaps) and DNA Ligase (adds phosphate in the remaining gaps of the phosphate - sugar backbone). Each new double helix is consisted of one old and one new chain. This is what we call semiconservative replication. 6

5)The lastthe TerminationPolymerase reaches to an end of the strands. We can easily understand that in the last section of the lagging strand, when the RNA primer is removed, it is not possible for the DNA Polymerase to seal the gap (because there is no primer). So, the end of the parental strand where the last primer binds isn't replicated. These ends of linear (chromosomal) DNA consists of noncoding DNA that contains repeat sequences and are called telomeresremoved in every cycle of DNA Replication.6)The DNA Replication is not completed before a mechanism of repairduring the replication. Enzymes likethe wrong nucleotides and the DNA Polymerase fills the gaps.Mitosis:daughter cells. Chromosomes do not pair up at equator. Diploid 2n (46).

Meiosis:cell division necessary for sexual reproduction. Chromosomes pair up at the equator. Haploid n (23).

Cytokinesis:  division of the cytoplasm and the plasma membrane following the division of the nucleus resulting into two cells, each having its own nucleus and cytoplasm surrounded by a plasma membrane.

Recombination:A process by which pieces of DNA are broken and recombined to produce new combinations of alleles.Pieces of DNA molecules are constantly being broken apart and exchanged with other DNA molecules. It is the formation of new allele combinations in a gamete. It results from two events in meiosis, independent assortment and crossing over. Independent assortment occurs in meiosis I when each pair of homologous chromosomes lines up on the metaphase plate. Each pair lines up independently of other pairs. In each pair the paternal chromosome may be on the left or right. The number of possible combinations of maternal and paternal chromosomes in the nuclei produced by meiosis equals 2 raised to the power of n, where n is the number of pairs of chromosomes. For the 23 pairs of human chromosomes this amounts to over 8 million combinations.

Aceto-orcein Staining for Chromosomes: - Good for the rapid count of chromosomesPlasma membrane/cell membrane disappears during Early Prophase? Nuclear membrane – surrounds nucleus while Plasma membrane/cell membrane surrounds the entire cell. Colour staining pattern you would expect to see under a fluorescence microscope:

Fluorescent dyes used for staining cells are detected with a fluorescence microscopeThe cell cycle, or cell-division cycle, is the series of events that take place in a cell leading to its division and duplication (replication) that produces two daughter cells. In cells without a nucleus (prokaryotic), the cell cycle occurs via a process termed binary fission. In cells with a nucleus (eukaryotes), the cell cycle can be divided in three periods: interphase—during which the cell grows, accumulating nutrients needed for mitosis preparing it for cell division and duplicating its DNA—and the mitotic (M) phase, during which the cell splits itself into two distinct cells, often called

"daughter cells" and the final phase, cytokinesis, where the new cell is completely divided. The cell-division cycle is a vital process by which a single-celled fertilized egg develops into a mature organism, as well as the process by which hair, skin, blood cells, and some internal organs are renewed.Animal cell cycleThe word "post-mitotic" is sometimes used to refer to both quiescent and senescent cells. Nonproliferative cells in multicellular eukaryotesgenerally enter the quiescent G0 state from G1 and may remain quiescent for long periods of time, possibly indefinitely (as is often the case for neurons). This is very common for cells that are fully differentiated. Cellular senescence occurs in response to DNA damage or degradation that would make a cell's progeny nonviable; it is often a biochemical reaction; division of such a cell could, for example, become cancerous. Some cells enter the G0 phase semi-permanentally e.g., some liver, kidney, stomach cells. Many cells do not enter G0 and continue to divide throughout an organism's life, e.g. epithelial cells.

InterphaseBefore a cell can enter cell division, it needs to take in nutrients. All of the preparations are done during interphase. Interphase is a series of changes that takes place in a newly formed cell and its nucleus, before it becomes capable of division again. It is also called preparatory phase or intermitosis. Previously it was called resting stage because there is no apparent activity related to cell division.Typically interphase lasts for at least 90% of the total time required for the cell cycle.Interphase proceeds in three stages, G1, S, and G2, preceded by the previous cycle of mitosis and cytokinesis. The most significant event is the replication of genetic material (DNA) in S phase.G1 PhaseThe first phase within interphase, from the end of the previous M phase until the beginning of DNA synthesis, is called G1 (G indicatinggap). It is also called the growth phase. During this phase the biosynthetic activities of the cell, which are considerably slowed down during M phase, resume at a high rate. This phase is marked by the use of 20 amino acids to form millions of proteins and later on enzymes that are required in S phase, mainly those needed for DNA replication. Duration of G1 is highly variable, even among different cells of the same species. It is under the control of the p53 gene. We can say that in this phase, cell increases its supply of proteins, increases the number of organelles (such as mitochondria, ribosomes), and grows in size.S PhaseThe ensuing S phase starts when DNA replication commences; when it is complete, all of the chromosomes have been replicated, i.e., each chromosome has two (sister)chromatids. Thus, during this phase, the amount of DNA in the cell has effectively doubled, though the ploidy of the cell remains the same. During this phase, synthesis is completed as quickly as possible due to the exposed base pairs being sensitive to harmful external factors such as mutagens.

Mitosis (M phase, mitotic phase)Main article: Mitosis

The relatively brief M phase consists of nuclear division (karyokinesis). It is a relatively short period of the cell cycle. M phase is complex and highly regulated. The sequence of events is divided into phases, corresponding to the completion of one set of activities and the start of the next. These phases are sequentially known as:

prophase , metaphase , anaphase , telophase cytokinesis  (strictly speaking, cytokinesis is not part of mitosis but is an event that directly follows

mitosis in which cytoplasm is divided into two daughter cells)Mitosis is the process by which a eukaryotic cell separates the chromosomes in its cell nucleus into two identical sets in two nuclei.[2] During the process of mitosis the pairs ofchromosomes condense and attach to fibers that pull the sister chromatids to opposite sides of the cell.[3] It is generally followed immediately by cytokinesis, which divides the nuclei, cytoplasm, organelles and cell membrane into two cells containing roughly equal shares of these cellular components. Mitosis and cytokinesis together define the mitotic (M) phase of the cell cycle - the division of the mother cell into two daughter cells, genetically identical to each other and to their parent cell. This accounts for approximately 10% of the cell cycle.Mitosis occurs exclusively in eukaryotic cells, but occurs in different ways in different species. For example, animals undergo an "open" mitosis, where the nuclear envelope breaks down before the chromosomes separate, while fungi such as Aspergillus nidulans and Saccharomyces cerevisiae (yeast) undergo a "closed" mitosis, where chromosomes divide within an intact cell nucleus.[4] Prokaryotic cells, which lack a nucleus, divide by a process called binary fission.Because cytokinesis usually occurs in conjunction with mitosis, "mitosis" is often used interchangeably with "M phase". However, there are many cells where mitosis and cytokinesis occur separately, forming single cells with multiple nuclei in a process called endoreplication. This occurs most notably among the fungi and slime moulds, but is found in various groups. Even in animals, cytokinesis and mitosis may occur independently, for instance during certain stages of fruit fly embryonic development. Errors in mitosis can either kill a cell through apoptosis or cause mutations that may lead to cancer. Cell Cycle SummaryInterphase is made up of three distinct phases: G1, S phase, and G2. The G1 and G2 phases serve as checkpoints for the cell to make sure that it is ready to proceed in the cell cycle. If it is not, the cell will use this time to make proper adjustments that can include cell growth, correction or completion of DNA synthesis, and duplication of intracellular components. S phase involves the replication of chromosomes. All three stages of interphase involve continued cell growth and an increase in the concentration of proteins found in the cell.

Biology SAC 3: Inheritance

The following key knowledge is the focus of this task: • Inheritance:– the nature of chromosomes, alleles, genotype and phenotype 

– the causes of phenotypic variation: mutations; recombination of parental alleles in sexual    reproduction; polygenes; and interactions of environmental factors with genes – patterns of inheritance involving the monohybrid cross: dominance; recessiveness; co-dominance;    multiple alleles – dihybrid crosses as independent – use of the test cross 

Inheritance: Genes and Inheritance:Genes contain info for production of proteins and functional RNA molecules. Proteinsresponsible for physical expression of genes as phenotypic characteristics or traits, such as eye colour. Since genes are inherited, traits are also inherited.

Inheritance of Traits: Sexual Reproduction: In organisms that reproduce sexually, traits are inherited though gametes. Gametes (sperm and eggs or pollen and ova) are produced by meiosis. Offspring possess a combination of genes from both parents. Example: haploid sperm and egg unite to form diploid zygote.

Asexual Reproduction: Barring mutation, offspring of organisms that reproduce asexually (without meiosis) are genetically

identical clones of the parent. In some exceptions, genetic material can be exchanged between clones. E.g. antibiotic resistance in

bacteria can be transferred via plasmid DNA. Example: bacteria reproduce asexually by binary fission.

Location of Genes: Position of gene on chromosome is the locus. In sexually reproducing organisms, most cells have homologous pair of

chromosomes (one from each parent). Chromosomes from homologous pair have genes that control the same trait at the

same locus.

Alleles: Genes occupying same position (locus) on homologous chromosomes are called alleles. Alleles are versions of the same gene that code for a variant of the

same polypeptide Any one individual can only have a maximum of two alleles for a given

gene There may be more than two alleles in a population, e.g. blood groups

A, B, O

Biology SAC 4 PreparationKey Knowledge: 1) A qualitative treatment of changing allele frequencies in a population and the consequences: The concept of gene pool

Gene pool refers to the genetic information (sum of all genes and their particular alleles) present in a population of organisms, and is expressed in terms of the frequencies (proportions) of the various alleles in a population. The gene pool of a population may change over time as a result of the following factors listed below.

Environmental selection pressures, gene flow, genetic drift (founder and bottleneck effects) - Selection pressures (survival of the fittest): - Migration - also known as gene flow: can change the allele frequencies of a population. Unlike

selection which requires several generations to have an effect, changes due to migration can occur very quickly.Emigration can also change allele frequencies if the emigrant group is not a representative sample of the original population. Imagine a small population that comprises mainly homozygous AA but a few heterozygous Aa and homozygous aa. If all the heterozygotes and the homozygous aa

organisms emigrate from this population, the allele frequencies are altered immediately. The gene pool now contains only one allele for the trait concerned. When only one allele is present in the gene pool of a population, the allele is said to be fixed.

- Genetic Drift – change in the gene pool of a population over succeeding generations by chance: Chance events can cause allele frequencies in a population to change over time. When chance effects operate, the direction of the change is unpredictable and can vary from one generation to the next. The resulting pattern of change is known as random genetic drift. The smaller the population size, the greater the potential impact of genetic drift. In a very small population, genetic drift can lead to the decrease, and eventual loss, of favourable alleles from the gene pool. For this reason, when a species is reduced to one or a few small populations, the species is at great risk of extinction. It may become extinct in spite of conservation measures.

Genetic drift is important when the size of a population is drastically reduced by a major calamity, such as a widespread fire or flood. The few survivors that reproduce to give the next generation may by chance be an unrepresentative sample of the original population. This is known as the bottleneck effect. Populations of macaroni penguins (Eudyptes chrysolophus) live on sub-Antarctic islands and on the Antarctic Peninsula. Most have black faces but a small proportion has white faces. On Macquarie Island, however, the population is composed almost entirely of the white-faced variety. How did this occur? It may be by chance that the small founder population of Macaroni penguins that first occupied Macquarie Island consisted only of the white-faced variety. So, when a small unrepresentative sample of a population leaves to colonise a new region, this is known as the founder effect.

Natural selection as a mechanism for biological evolutionNatural Selection: action of any environmental factor that acts on a population in the wild to result in differential reproduction. Differential reproduction occurs when one inherited phenotype in a population produces more viable offspring than other phenotypes, hence making a greater contribution to the gene pool of the next generation.

Darwin’s process of natural selection has four components:- Variation. Organisms (within populations) exhibit individual variation in appearance and behavior.

These variations may involve body size, hair color, facial markings, voice properties, or number of offspring. On the other hand, some traits show little to no variation among individuals—for example, number of eyes in vertebrates.

- Inheritance. Some traits are consistently passed on from parent to offspring. Such traits are heritable, whereas other traits are strongly influenced by environmental conditions and show weak heritability.

- High rate of population growth. Most populations have more offspring each year than local resources can support leading to a struggle for resources. Each generation experiences substantial mortality.

- Differential survival and reproduction. Individuals possessing traits well suited for the struggle for local resources will contribute more offspring to the next generation.

2) Evidence for biological evolution over time: Evolution is a process of change. Changes in the environment lead to living organisms gradually changing and developing new features (due to a change in the genetic make-up) to better suit the new environmental conditions (adaptations).

This process happens slowly over many generations and years. It is believed that evolution began in water with a single celled organism that became multi-cellular due to errors in cell division process. This eventually lead to cell specialization where different cells carried out a particular function and gradually to the formation of tissues, organs and systems in more complex organisms. Evolution: Changes over time The Modern Theory of Evolution states that: - All living organisms today share a common origin - The earliest organism resembled bacteria that are living today - Over time different organisms diverged from early forms of life - Some became extinct whilst some evolved

Evidence for Biological Evolution Over Time Evidence for Evolution Definition Examples Fossil record Transitional fossils Comparative anatomy Comparative embryology Homologous features Analogous features Cell processes DNA similarity in gene sequences DNA hybridization Chromosomes Genetic linkage

The geological time scale; relative and absolute dating techniques Geological time scale: The geologic time scale (GTS) is a system of chronological measurement that relates stratigraphy to time, and is used by geologists, palaeontologists, and other earth scientists to describe the timing and relationships between events that have occurred throughout Earth's history. The table of geologic time spans presented here agrees with the nomenclature, dates and standard colour codes set forth by the International Commission on Stratigraphy.The geological time scale is based on the geological rock record, which includes erosion, mountain building and other geological events. Over hundreds to thousands of millions of years, continents, oceans and mountain ranges have moved vast distances both vertically and horizontally. For example, areas that were once deep oceans hundreds of millions of years ago are now mountainous desert regions.

Absolute dating techniques: Absolute dating is the process of determining an approximate computed age in archaeology and geology. Some scientists prefer the terms chronometric or calendar dating, as use of the word "absolute" implies an unwarranted certainty and precision.[1][2] Absolute dating provides a computed numerical age in contrast with relative dating which provides only an order of events.

In archaeology, absolute dating is usually based on the physical or chemical properties of the materials of artefacts, buildings, or other items that have been modified by humans. Absolute dates do not

necessarily tell us precisely when a particular cultural event happened, but when taken as part of the overall archaeological record they are invaluable in constructing a more specific sequence of events.

Relative dating techniques: Relative dating is the science of determining the relative order of past events, without necessarily determining their absolute age. In geology rock or superficial deposits, fossils and lithologies can be used to correlate one stratigraphic column with another. Prior to the discovery of radiometric dating which provided a means of absolute dating in the early 20th century, archaeologists and geologists were largely limited to the use of relative dating techniques to determine the age of geological events.

Though relative dating can only determine the sequential order in which a series of events occurred, not when they occur, it remains a useful technique especially in materials lacking radioactive isotopes. Relative dating by biostratigraphy is the preferred method in palaeontology, and is in some respects more accurate (Stanley, 167–69). The Law of Superposition was the summary outcome of 'relative dating' as observed in geology from the 17th century to the early 20th century.

The fossil record; biogeography; comparative morphology; molecular homologyFossil Record: Our window to life on Earth in the geological past is through fossils. They provide evidence of the kinds of organisms that lived on Earth. Fossil evidence may be: - Direct evidence such as bones, teeth, leaves and shells - Indirect evidence such as footprints, tooth marks, tracks, burrows and coprolites (fossilised shit).

Indirect signs are called trace fossils and sets of dinosaur footprints (trackways) are the best known among them. When organisms die, microbial action causes their decomposition and a after a period of time, no trace remains. However every rarely, the remains of the organism are preserved long after death, and this process of preservation is known as fossilisation.

Biogeography: Biogeography is the study of the distribution of species and ecosystems in geographic space and through geological time. Organisms and biological communities vary in a highly regular fashion along geographic gradients of latitude, elevation, isolation and habitat area.

Homology: Similar Structures – the first mammals appeared about 200 Myr ago and are believed to have evolved from a reptilian ancestor

3) Determination of evolutionary relationships: Comparison of DNA sequences; comparative genomics; mitochondrial DNA; phylogeny

4) Patterns of biological change: Allopatric speciation Divergent and convergent evolution

Divergent Evolution: When closely related species become more dissimilar over time, usually in response to different environmental conditions and different selection pressures. Convergent Evolution: The development of similar features separately in unrelated groups of organisms, which resulted in the two species, become more alike or converges. Example: Llama and camel, lion and jaguar.Parallel Evolution: when related species evolve similar features independently. Example: bilby and marsupial mole both have backward opening pouches due to burrowing behaviour.

Extinctions