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Joe Lecture 1

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Buffers minimise pH changes: Cells must maintain stable pH to maintain functions. Blood is pH 7.4, buffered by carbonic acid. The 7 most important functional groups for the chemistry of life: Hydroxyl Carbonyl Carboxyl Amino Sulfhydryl Methyl Phosphate ATP reacts with H2O to produce ADP and an inorganic phosphate. Molecules are assembled by dehydration reaction: Requires energy (ATP) and enzymes. Reaction releases H2O. Molecules are disassembled by hydrolysis: H2O required to break covalent bond. Releases energy stored in bonds. Amino acids all have same basic structure: Amino group, carboxyl group and a varying side R group. Amino acids are characterised by their side group Non-polar (hydrophobic), Polar (uncharged) or Ionisable. Protein structure: The sequence of amino acids determines a protein s 3D structure. A protein s structure determines its function. Tertiary structure based on R-group interactions.

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y Chaperonins help proteins fold into the correct 3D shape: 1. An unfolded polypeptide enters cylinder from one end. 2. The cap attaches, causing the cylinder to change shape in such a way it creates a hydrophilic environment for the folding of the polypeptide. 3. The cap comes off and the correctly folded protein is released.

Joe Lecture 2
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Pyrimidines C and T: have a single six-membered ring. Purines G and A: has a six-membered ring fused with a five-membered ring. Equal portion of pyrimidines and purines. If a section of DNA has more G-C bonds then it will have a higher melting point than normal due to the more 3 hydrogen bonds present. Carbohydrates store energy and provide building materials. Includes simple sugars and their polymers which are rich in the energy storing C-H bonds. Disaccharides are commonly used for sugar transport. Two sugars joined by glycosidic bond. Starch = 1-4 linkage of alpha glucose monomers. Cellulose = 1-4 linkage of beta glucose monomers.

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Lipids are a diverse group of hydrophobic molecules. Fats, oils, waxes, phospholipids and steroids that contain nay C-H bonds. Saturated fatty acids have the maximum number of hydrogen atoms possible and no double bonds. Unsaturated fatty acids have one or more double bond. Fats are useful for energy storage, cushioning organs and body insulation. Phospholopids made up membranes. They a polar head (hydrophilic) and 2 non -polar tails made up of fatty acids (hydrophobic). Spontaneously forms a bilayer in water. Membranes the plasma membrane exhibits selective permeability. Cell fusion experiments show that cell membranes are fluid. Membrane proteins float in a lipid bilayer. Less fluidity at lower temperatures. More fluidity with more unsaturation of fatty acid. The steroid cholesterol has different effects on membrane fluidity at different temperatures: At warm temperatures (around 37 degrees) cholesterol restrains movement of phospholipids. At cooler temperatures, it maintains fluidity by preventing tight packing. Six major functions of membrane proteins: 1) Transport 2) Enzymatic activity 3) Signal transduction 4) Cell-cell recognition 5) Intercellular joining 6) Attachment to the cytoskeleton and extra-cellular matrix.

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Joe Lecture 3
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Only hydrophobic molecules (such as O2, hydrocarbons or CO2) can pass through the phospholipid bilayer. Polar molecules/ions (H2O, glucose, Na+) require means of transport into cell this is provided by proteins. Transport proteins allow passage of hydrophilic substances across the membrane. Transmembrane proteins span lipid bilayer. Two modes of membrane transport: Passive (includes diffusion) and active (requires energy). Osmosis is the diffusion of water across a selectively permeable membrane. Water diffuses from lower solute concentration to the region of higher solute concentration (water concentrations opposite to solute). Tonicity is the ability of a solution to cause a cell to gain or lose water. Isotonic solution: no net water movement across plasma membrane. Animal = Normal. Plant = Flaccid. Hypertonic solution: cell losses water. Animal = shrivelled. Plant = Plasmolyzed. Hypotonic solution: cell gains water. Animal = Lysed. Plant = Turgid. Osmoregulation is the process of extrusion of water in cells. Water is collected into a vacuole and pumped out.

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Uses of active transport: Accumulate solutes in cells, extrude solutes into extracellular fluid, generate electric gradient across cell membrane, generate concentration gradients across cell membrane electrochemical gradient, gradients can do work cotransport. y Sodium/potassium pump: 1. Cytoplasmic Na+ binds to the sodium-potassium pump protein. 2. Na+ binding stimulates phosphorylation by ATP.
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3. Phosphorylation causes the protein to change its shape and Na+ is released to outside. 4. K+ binds on the extra-cellular side and triggers the release of the phosphate group left by the ATP reaction to ADP. 5. Loss of the phosphate group restores the original shape of the protein. 6. K+ is released and the cycle repeats. y Proton pump actively transports H+ against its concentration.
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Endocytosis is the transport of bulk materials into the cell by creating a vesicle around the material. 3 types of endocytosis: Phagocytosis uptake of particles (unicellular eating), Pinocytosis Uptake of small molecules and receptor-mediated endocytosis molecule binds to the receptor protein on cell surface and the binding stimulates endocytosis. Exocytosis is the transport of bulk materials out of the cell by the vesicle fusing with the membrane to release material.

Joe Lecture 4
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The cytoskeleton is a network of fibres that organises structures and activities in the cell. It contains three types of proteins that form the structural components: Mircrotubules, microfilaments and intermediate filaments. The cytoskeleton supports cell shape and anchors organs. It is also important for movement and transport: within cells, into cells (endocytosis) and of cells. Three major cytoskeleton fibres: Actin filaments, Intermediate filaments and microtubules. Actin: Two intertwined strands of actin. Maintenance of cell shape, changes in cell shape, muscle contraction, cytoplasmic streaming, cell motility and cell division. Dynamic: length is changed by addition or removal of actin subunits. Required for cell shape: cell motility, cell division cytokinesis (contractile ring), muscle contraction and cytoplasmic streaming. Actin sliding is required for cytokinesis in animals. Muscle contraction uses sliding filament mechanism: Attached: Head bound to myosin. Released: Binding of ATP, releases myosin head. Cocked: Hydrolysis of ATP causes configuration change, myosin bends . Force: Attachment of myosin to new actin site, release of ADP leads to myosin shape to change back to normal. Repeats. 2+ Ca2+, troponin and tropomyosin control skeletal muscle contraction: When no Ca is present the troponin complex and the tropomyosin blocks the myosin binding sites on the actin. But when Ca2+ is present it binds with the troponin protein and moves the tropomyosin out of the way. Muscle contraction utilises passive and active Ca2+. Intermediate filaments: Fibrous proteins supercoiled into thicker cables. Maintenance of cell shape, anchorage of nucleus and certain other organelles, formation of nuclear lamina. Mircotubules: Hollow tubes; walls consists of 13 columns of tubulin molecules. Maintenance of cell shape, cell motility, chromosome movement on cell division, organelle movement. Microtubules are required for chromosome division (the mitotic spindle). As with Actin, microtubules can undergo treadmilling with addition of tubulin heterodimers at the plus end and the subtraction at the minus end.

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Mitotic spindle: Set of mircotubules originating from the microtubule organising centre (MTOC) centrosome. y In animals/protists MOTC contains centrioles. Plants have none. y There are 3 sets of mircotubules originating from the MOTC: 1. Kinetochore attaches to the chromosomes. 2. Polar overlap between 2 centrosomes 3. Unattached (astral) stabilizing. Microtubules are found in Eukaryote flagella and cilia. Cilia are used for swimming and moving fluids and particles. Some toxins and drugs affect the ploymerisation or depolymerisation of tubulin: Taxol: stabilizes microtubules and prevents depolymerisation by binding to a specific site on beta-tubulin proteins. Nocodazole: causes depolymerisation of mircotubules.

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Joe Lecture 5
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The ability of organisms to reproduce distinguishes living things from non-living matter. Cell division has two processes: Mitosis and cytokinesis. In unicellular organisms, division of one cell reproduces the whole organism. Multi-cellular organisms depend on cell division for development, growth and repair. Every eukaryotic species has a characteristic number of chromosomes in each cell nucleus. Somatic cells are non-reproductive cells. Gametes (sperm and egg) are reproductive cells. Eukaryotic chromosomes consist of a chromatin. In preparation for cell division, DNA is replicated and the chromosomes condense. Each duplicated chromosome has two sister chromatids, which separate during during ce ll division. The centromere is the narrow waist of the duplicated chromosome, where the two chromatids are most closely attached. Eukaryotic cell division consists of mitosis (the division of the nucleus) and cytokinesis (the division of the cytoplasm. Gametes are produced by a variation of cell division called meiosis. Meiosis yields non-identical daughter cells that only have one set of chromosomes. The cell cycle consists of mitotic phase (mitosis and cytokinesis) and the interphase (cell growth and copying of chromosomes in preparation for cell division). Interphase (90%) can be divided into subphases: G1, S (synthesis), and G2. The cell grows during all three phases but chromosomes are duplicated only during S phase. Mitosis is conventionally divided into 5 phases: prophase, prometaphase, metaphase, anaphase and telophase. The mitotic spindle: The centrosome replicates, forming two centrosomes that migrate to opposite ends of the cell, as the spindle microtubules grow out from them. During prometaphase some mircotubules attach to the kinetochores of the chromosomes and begin to move the chromosomes. At metaphase the chromosomes are all lined up at the metaphase plate.

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Cytokinesis is the division of the cytoplasm. Animals = cleavage furrow. Plants = Cell plate (phragmoplast). The eukaryotic cell cycle is regulated by a molecular control system or chemical signals. The clock has specific checkpoints where the cell cycle until a go-ahead signal is received. Two types of regulatory proteins are involved in cell control: cyclins and cyclin-dependant kinases (Cdks). MPF (maturation-promoting factor) is a cyclin-Cdks complex that triggers a cell to enter the Mitosis phase.

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Joe Lecture 6
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Watson and Crick s semi-conservative model of replication predicts that when a double helix replicates, each daughter molecule will have one old strand and one newly made strand. Meselson and Stahl used N isotopes to test the 3 models. Helicases are enzymes that untwist the double helix at the replication forks. Single-strand binding protein binds to and stabilizes single-strand DNA until it can be used as a template. Topisomerase corrects over-winding ahead of replication forks by breaking, swivelling and rejoining DNA strands. DNA polymerase cannot initiate synthesis of a polynucleotide. Primase is needed to add a short primer on so polymerase III is able to add bases to the 3 end. Ligases join DNA backbone and Okazaki fragments. Polymerase I removes RNA primers and fills in the gaps. Telomeres are tandem repeats at ends of chromosomes. Lagging strand cannot be synthesised at telomeres. Telomeres get shortened every replication. Fixed only in reproductive cells.

Joe Lecture 7
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Central dogma of gene expression: DNA -> RNA -> Protein. Alternative versions of a gene are called alleles. Each gene resides at a specific locus on a specific chromosome. Each characteristic an organism inherits there are two alleles, one from each parent. If two alleles at a locus differ then the dominant allele determines the organism s phenotype and the recessive allele has no effect on appearance. Phenotype is the physical appearance. Genotype is the genetic makeup. George Beadle and Edward Tatum developed the one gene one enzyme hypothesis. Basic principles of transcription and translation: RNA is the intermediate between genes and proteins they code. Transcription is the synthesis of RNA under the direction of DNA. Transcription produces mRNA. Translation is the synthesis of a ploypeptide, which occurs under the direction of mRNA. Ribosomes are the sites of translation. RNA synthesis is catalysed by RNA polymerase, which pries the strands apart and hooks together the RNA nucleotides. Bases pair up with uracil replacing thymine.

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Eukaryotic cells modify RNA after transcription. During RNA processing, both ends of the primary transcript are usually altered. The 5 end receives a modified nucleotide 5 cap. The 3 end gets a poly-A tail. These modifications help facilitate the export of mRNA, protect mRNA from hydrolytic enzymes and help the ribosomes attach at the 5 end. Non-coding Introns are spliced out of the mRNA and creates a continuous coding sequence of exons. Spliceosomes consist of a variety of proteins and several small nuclear ribonucleoproteins that recognise the splice sites which contain functional RNA molecules. Some genes can encode more than one kind of polypeptide, depending on which segments are treated as exons during RNA splicing called alternative splicing. Because of alternative splicing the number of different proteins an organism can make is much greater than the number of genes. Of the 64 triplets or codons, 61 are for amino acids and 3 are for stop codons to stop translation. The genetic code is redundant but not ambiguous therefore no codon specifies more than one amino acid. Codons must be read in the correct reading frame. Molecules of tRNA are not identical: Each carries a specific amino acid on one end and the corresponding anticodon on the other. Ribosomes facilitate specific coupling of tRNA anticodons and mRNA codons. The two ribosomal subunits are made up of proteins and ribosomal RNA. The P site holds the tRNA that carries the growing polypeptide chain. The A site holds the tRNA that carries the next amino acid to be added to the chain. The E site is the exit site where used tRNA leaves the ribosome.

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Joe Lecture 8
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To initiate transcription, eukaryotic RNA polymerase requires the assistance of proteins called transcription factors. High levels of transcription of particular genes depend on control elements interacting with specific transcription factors. Proximal control elements are located close to the promoter. Distal control elements, groups of which are called enhancers, may be far away from a gene or even located in an intron. An activator is a protein that binds to an enhancer and stimulates transcription of a gene. Bound activators cause mediator proteins to interact with proteins at the promoter. Some transcription factors function as repressors, inhibiting expression of a particular gene. Cancer results from genetic changes that affect cell cycle control. Oncogenes are cancer causing genes. Proto-oncogenes are the corresponding normal cellular genes that are responsible for normal cell growth and division. Conversion of a proto-oncogene to an oncogene can lead to abnormal stimulation of the cell cycle. Tumor-suppressor genes help prevents uncontrolled growth.

Tumor-suppressor proteins repair damaged DNA, control cell adhesion and inhibits the cell cycle in the cell-signal pathway. Multiple mutations are generally needed for fully-fledged cancer. At the DNA level, a cancerous cell is usually characterised by at least one active oncogene and the mutation of several tumor-suppressor genes. Individuals can inherit oncogenes or mutant alleles of tumor-suppressor genes. Mutations in the BRCA1 or BRCA2 (tumor-suppressor genes) are found in at least half of inherited breast cancers. Mutations in BRCA2 lead to non-functional proteins, causing DNA damage to go unfixed increased risk of cancer. Also leads to other cancers ovarian, prostate and malignant melanoma. A gene is the unit of heredity made of DNA (or RNA) that encodes a coherent set of potentially overlapping functional product molecules, either protein or RNA, that influences phenotype in ways that we may or may not be able to measure.

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