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Chapter 1-4


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Biological Sciences
Stephen Reid

Cells: Rayana Alawie 1.1 The Discovery of Cells: Robert Hooke: Discovered cells by looking through a microscope at cork cells Leeuwenhoek: the first to examine a drop of pond water under the microscope and observe the teeming microscopic “animalcules” = bacteria. Matthias Schleiden: (1839) a German lawyer turned botanist concluded that plants were made of cells and that the plant embryo arose from a single cell. Schwann concluded that the cells of plants and animals are similar structures and proposed these two tenets of the cell theory:  All organisms are composed of one or more cells.  The cell is the structural unit of life. Rudolf Virchow, a German pathologist, had made a convincing case for the third tenet of the cell theory:  Cells can arise only by division from a preexisting cell. 1.2 Basic Properties of cells: Cells are the smallest units of life. Death is most basic property of life. Cells obtained from a tumor called HeLa cells (by George and Martha Gey): became the first human cells to be kept in culture for a long time. (grown in vitro = outside the body ina cultural medium)  Cells are Highly complex and Organized: o More complex= less tolerance of errors. o Complex structure matches the function of the cells o Ex epithelial cells lining the intestine have microvilli on the apical ends of the cells that facilitate the absorption of nutrients. Apical ends have protein actin to help project the microvilli outward. Basal end = a lot of mitochondria  Cells Possess a Genetic Program and the means to use it: o Information is packaged into a set of chromosomes that occupies the space ofa cell nucleus o Gene store and contain info. For constructing cellular structures. o Mutations lead to biological evolutions  Cells are capable of producing more of themselves: o Most cells reproduce via mitosis into daughter cells. o Some cells (oocytes) undergo division were only half genetic material is distributed.  Cells Acquire and utilize energy: o Light energy is converted by photosynthesis into chemical energy that is stored in energy-rich carbohydrates, such as sucrose or starch. o Cells expend an enormous amount of energy simply breaking down and rebuilding the macromolecules and organelles of which they are made. (turnover in order to maintain integrity of cell components.) Cells: Rayana Alawie  Cells Carry out a variety of chemical reactions: o Via enzymes. o Sum of chemical reactions in a cell = Metabolism.  Cells engage in mechanical Activities: o Materials are transported, assembled and disassembled and in many cases the cells actually move. Motor Proteins.  Cells are able to respond to stimuli: o Receptors help cells interact with other cells and the environment.  Cells are capable of self regulation: o Most evident when cells break down. o EXP: Hans Driesch, a German embryologist, found that he could completely separate the first two or four cells of a sea urchin embryo and each of the isolated cells would proceed to develop into a normal embryo.  Cells Evolve: o Thought that cells evolved from a pre-cellular life form which evolved from nonliving organic materials. 1.3 Two Fundamentally Different Classes of Cells: 1) Prokaryotic: (pro-before; karyon-nucleus) - Ex: Bacteria, Cyanobacteria - Structurally simpler. 2) Eukaryotic: (Eu- true) - Ex: Protists, Fungi, Animals, Plants - Structurally more complex Similarities between Eukaryotes & Prokaryotes: o Both types of cells share common structural features -cell membrane, cell walls (same function, different chemical composition): Ribosomes: Non membrane bound that help make protiens. o Both types of cells share an identical genetic language o Both types of cells share a common set of metabolic pathways (photosynthesis and protein synthesis, glycolysis, TCA cycle) o ATP located in the plasma membrane of prokaryotes and the mitochondrial membrane of eukaryotes) o Proteasomes (protein digesting structures) of similar construction (between archaebacteria and eukaryotes) Characteristics That Distinguish Eukaryotes From Prokaryotes o Eukaryotic cells are internally much more complex (structurally and functionally) Cells: Rayana Alawie - Ex: ER= cell’s protein and lipids are manufactured. , Golgi= materials are sorted modified and transported., Lysosomes, Endosomes, Peroxisomes, glyoxisomes, mitochondria, chloroplast, flagella, cilia - Prokaryotes have nucleoid (poorly demarcated cell region) o Eukaryotes have complex cytoskeletal system - Contains microfilaments, microtubules and motor proteins, Endo and phagocytosis. o Most eukaryotes have significantly more DNA : - Prokaryotes have a single circular chromosome. - Eukaryotes DNA is tightly compressed into chromatin. o No mitosis or meiosis in prokaryotes: In eukaryotes: - Presence of 2 copies of genes per cell (diploid) - Uses micro tubules - Prokaryotes can reproduce non sexually except conjugation (forms bridge “pilus” and exchange genes) Types of Prokaryotic Cells: 1) Archaebacteria: a. Extremophiles: live in inhospitable environemnts b. Methanogens: Convert CO2 and H2 into methane c. Halophiles: Love salty environments d. Acidophiles: Love acidic environments e. Thermophiles: Love high temp. environments f. Hyperthermalophiles: live in hydrothermal vents of the ocean floor 2) Bacteria (Eubacteria): a. Mycoplasma: smallest known cells b. Cyanobacteria: most complex contain membranes similar to those of the membranes of a chloroplast therefore they can photosynthesize by splitting the water. Also Nitrogen fixation chloroplasts evolved from symbiotic cyanobacteria Types of Eukaryotic cells: Cell Specialization: Eukaryotic cells are believed to be descended from prokaryotic cells – Endosymbionts (via phagocytosis) 1) Unicellular Organisms: 2) Multicellular Organisms: a. Differentiation: process of specializing cells i. Pathway of differentiation followed by each embryonic cell depends on the signals it receives from the surrounding environment. ii. Result: Different cells structure = Specialized functions. iii. Ex: red Blood cell = disc shaped + haemoglobin to transport oxygen iv. The #, appearance and location of the various organelles can be correlated with the activities of the particular cell type. v. Cells will have the same “house-keeping” Proteins for metabolism Aerobic Prokaryote (+mitochondrion)  Aerobic heterotrophic prokaryote (+membrane invagination)  Pro-eukaryotic cell (+ER) Protist Fungal animal cells (+Photosynthetic cyanobacterium) Algal and plant cells Cells: Rayana Alawie The Sizes of Cells and Their Components - Micrometers/ Micron (μm; = 10-3mm): Ex Mmitochondion, bacteria, epithelial cell - Nanometer (nm; = 10 mm): Ex Ribosome, Myoglobin, DNA - Angstrom (Å; 10 mm): Ex Water molecule 1.4 Viruses: Dimitri Ivanovsky: forced sap from a diseased plant through filter paper. The filter paper was still infective which led him to conclude that there are pathogens smaller than the smallest bacteria known as viruses: obligatory intracellular parasites. Properties of a virus: - Cannot reproduce, metabolize outside of host cell. - Virion: contains small amount of genetic material (RNA/DNA) - Virion is surrounded by a capsid. Capsid is made up of subunits arranged in polyhedron. - Some have wide host range but most are more specific. Bacteria viruses = Bacteriophages: most complex and most abundant. Two types of infection: Lyses: cell ruptures and releases a new generation of viruses Lytic: does not lead to the death of the host but integrates its DNA into the DNA of the host cell. (integrated viral DNA = provirus) . Some proviruses behave normally until exposed to a stimulus, light, heat. Some animal cells containing a provirus lose control over their own growth and division and become malignant (tumour virus). Some provirus can produce other provirus (HIV) Viroids: Smaller than a virus and contains a circular RNA and lacks a protein coat. CHAPTER 2:BIOCHEMISTRY The Nature of Biological Molecules biochemistry centers around carbon-binds to up to four other atoms since it has only4 outer electrons (8 needed to fill shell) organic molecules: called biochemical Types of Molecular Bonds in Biochemistry I. Covalent Bonds-electron pairs are shared between atoms to make molecules -The number of covalent bonds formed is determined by the number of electrons needed to fill outer shell -atoms are most stable with a full outer electron shell Covalent Bonds can lead to A) Polar Molecules B) Non Polar Molecules C) Ionized Atoms Cells: Rayana Alawie A) Polar Molecules: -atom will become relatively electronegative compared to other atom -unequal sharing of electrons If nucleus more positively charged on one atom -will attract electrons more B) Non-Polar Molecules -equal sharing of electrons -Molecules without electronegative atoms & polar bonds (those consisting of C & H) are nonpolar C) Ionized Atoms -an atom is so strongly electronegative that it can capture electrons from another atom II. Non-Covalent Bonds-Govern interactions between molecules or different parts of a large biological molecule -such bonds are typically weaker linkages i. Ionic Bonds ii. Hydrogen Bonds iii. Hydrophobic Interactions i) Ionic Bonds-atoms/molecules with positive & negative charges that attract each other -can hold macromolecules together (DNA-protein) ii) Hydrogen Bonds eg. Water -occurs between polar molecules= HYDROPHILIC -the partially positive H on one water molecule interacts with the negatively charged O on the second water molecule iii) Hydrophobic Interactions -non-polar molecules are not charged and cannot interact with water -form aggregates to minimize exposure to polar surroundings Macromolecules Hydrocarbons: -contain only hydrogen and carbon atoms (build around carbon) -Form carbon-containing backbones which may be linear, branched or cyclic -Hydrogen often replaced by functional groups -Double bonds + triple bonds: the bonds can’t rotate. Single bonds are more flexible. Functional groups:  Hydroxyl [-OH] = alcohols  Carboxyl [-COOH] = acids  Amino [-NH2]  Sulfhydrl [S-H] : sulphide double bonds on each other.  Phosphate ESTER BONDS: - Arises from a reaction between an acid and alcohol with the elimination of water. - (P-O-C) Phosphate ester linkage attaches a phosphate group to a lipid Cells: Rayana Alawie - In DNA and RNA successive nucleotides are held together by 3’-5’ phosphodi-ester bonds *3’ C-O-P-O-5’C+ - Acid [COOH]+ Alcohol [-OH]  Ester +h2O 9dehydration reaction) AMIDE/PEPTIDE BOND: - Forms amino acids - Amino group of one amino acid joins to the carboxyl group of another amino acid, through elimination of water - Creates peptide chains. - Acid [COOH] + Amine [NH]  Amide +H2O (dehydration reaction) - Importance of Functional Groups: -generally have one or more electronegative atoms(N, P, O and/or S) -makes organic molecules more polar,and more reactive -many are capable of ionization & may be + or –in charge Four Types of Biological Macromolecule/ Polymer Monomer Carbohydrate Monosaccharide Nucleic Acid Nucleotides Lipids Glycerol + Fatty acid Proteins Amino acid Formation of Macromolecules - Monomers are joined by condensation reaction  where a water molecule is removed - Polymers are broken down by hydrolysis-a water is added Carbohydrates/Sugars: (CH2O)n o Function:  -stores chemical energy  -structural function-exoskeleton of insects, plant cell wall  -attaches to plasma membrane lipids and proteins  -glycocalyx  -important for cell recognition and cell identity  Eg: blood types: A,B,Etc. o Linkage:  -Sugars with 5 or more carbons convert into closed, ring-containing molecule  -Linking sugars together -from covalent bond between C1 of one sugar and OH of another called glycosidic linkage  -Important sugars in cell metabolism have from 3-7 carbons  -Energy stored in H atoms : used in mitochondria o Types of Carbohydrates:  Disaccharide-2 monosaccharides covalently bond together  for energy stores  eg. sucrose (table sugar), lactose and maltose Cells: Rayana Alawie  Oligosaccharides-small chains of sugars (oligo-few)  usually attached to lipids & proteins converting them to glycolipids& glycoproteins => GLYCOCALYX  Polysaccharides-many sugars hooked together; very large molecules. : Store energy  Glycogen: Liver cell to store energy. Paralleled vertically 3-D structure  Starch: Plants store energy. Linear monomers then coils.  Cellulose: Sheets of monomer- parallel: Plant cell walls  Chitin: exoskeleton of invertebrates Nucleic Acids: - Structure:  Both DNA & RNA are composed of nucleotides (phosphate + sugar + base) connected to form polymers (polynucleotides)  Phosphate group (PO4-) -linked to 5'-carbon of sugar  5-carbon sugar-ribose or deoxyribose.  Nitrogenous base -nitrogen atoms form part of the rings of the molecules -Purines: Guanine, Adenine = double ring -Pyrimidine: Cytosine , Thymine (uracil) = single ring -Guanine + Cytosine : TRIPLE BOND -Adenine +Thymine: DOUBLE BOND - Bases are joined together by H-bonds.  Backbone = Phosphate+ Sugar. o Linkage:  Monomers polymerize when OH on sugar of one nucleotide binds covalently to phosphate of next nucleotide in chain  nucleotides are joined by sugar-phosphate linkages: Phosphodiester bonds  to make each DNA strand and RNA strand (single stranded) then the 2 strands wrap around each other with hydrogen bond o Types of Nucleic acid:  DNA:  Serves as a genetic material of all cell organisms Cells: Rayana Alawie  Information sotred in DNA used to govern activities through formation of RNA messages  RNA:  Ribosomal RNA (rRNA)  Transfer RNA (tRNA)  Messenger RNA (mRNA)  ATP:  Adenosine triphosphate is an RNA nucleotide -source of energy for biochemical reactions (most of energy being used at any given moment in any living organism is derived from it)  energy comes from ATP hydrolysis to create ADP + Pi  release of phosphate releases energy  GTP:  Guanosine triphosphate: important for function of many proteins  binds to a variety of proteins (called G proteins) & acts as a switch to turn on their activities  Hydrolysis of GTP  GDP + Pi : releasing energy. Lipids: (composed of C,H,O) o Types:  Triglyceride:  Amphipathic: It is both polar and non polar  Composed of 3 fatty acids (non-polar) + glycerol (polar)  Used for fuel  Stored in adipocytes  LINKED BY ESTER BOND  Steroids:  Complex ring structures:  Eg: Cholesterol: important in plasma membrane – building block for many steroid hormones. Eg: testosterone (has double bond in one end) , Estrogen Cells: Rayana Alawie (has hydroxyl group in one end) NOT PRESENT IN PLANT CELLS: “cholesterol free”  Phospholipids:  Glycerol + 2 fatty acids + phosphate group  Major cellular function: - Component of plasma membrane and organelle membranes - Barrier to water - Signalling on membrane - Has a polar head and a nonpolar tail forming = AMPHIPATHIC - Arrange into a bilayer - Hydrophobic portions on the interior - Saturated lipids = maximum component of single bonds no double/ triple - Unsaturated = double bonds there are kinks in the bonds Proteins: - Human Genome project: predicts ~ 30,000 orteins are manufactured from genes. Typical cell: makes 10,000 proteins. o Functions:  Enzymes: catalyze and accelerate rate of metabolic reactions  Signalling proteins: Kinases, phosphates , G-proteins  Hormones, growth factors  Gene activators / transcription factors  Membrane receptors and transporters  Cytoskeletal elements: giving cells shape, move and contract  Antibodies secreted by B-cells. o Where do proteins begin their life?  Gene is transcribed in nucleus  mRNA  Proteins are synthesized from mRNA by ribosomes : Translation  mRNA associates with ribosome (rRNA + protein)  tRNA brings in an amino acid: has specific amino acid for each anti codon on the tRNA  anticodon matches codon in mRNA  Codon = 3 nucleotide sequence in mRNA o Structure:  Composed of H, C, O, N & usually S or P  Basic monomer is amino acid: 20 types  Amino acid-backbone is a-carbon betweenNH2& COOH groups  Peptide bonds form through condensation reactions attaching carboxyl group of 1 amino acid to amino group of another  Forms polypeptide chains (proteins) Cells: Rayana Alawie  R Groups:  Give amino acids their variability  Determine inter-intramolecular interactions that determine molecular structure and protein activities  4 amino acid/ R group categories  Polar Charged - Can form ionic bonds - Histones with arginine (+charge) binds to –ve DNA - Hydrophilic side chains can act as acids or bases which tend to be fully charged - Side chains under physiological conditions are fully charged - Ex: Aspartic acid, Glutamic acid, Lysine arginine , Histidine  Polar uncharged : - R groups weakly charged - Can form H bonds - Ex: Serine, threonine, Glutamine, Asparagine, Tyrosine  Non-Polar: - R groups are large hydrocarbons - Hydrophobic - Usually in core of protein or within membranes away from water - Ex: alanine, valine, leucine, isoleucine, methionine, phenylanine, tryptophan  Others: - Cysteine: though side chain has a polar uncharged character it can form a covalent bond with another cysteine to form a DISULFIDE LINK - Glycine: can be either hydrophobic or hydrophilic - Proline: has hydrophobic character it can still create kinks in polypeptide chains and distort secondary structure o Levels of Protein Structure:  Primary Structure:  specific linear sequence of amino acids in chain  fron nucleotide sequence in gene of protein  20 variations of proteins  N= # of a.a and varies between proteins. It is not random. Similar functions between different organisms most probably have a similar protein structure.  sequence contains most, if not all, information needed to specify protein 3D shape, protein targeting & protein function  ex: sickle cell anemia: they clog small blood vessels and interfere with oxygen delivery. Results from a change in primary sequence. Glutamic acid (charged polar a.a) -> valine (non polar amino acid) result of Point mutation= one amino acid change.  Secondary Structure:  Conformation of polypeptide chain segments Cells: Rayana Alawie  arranged to make the maximum number of H bonds between neighbouring amino acids  i) alpha-helix: forms cylindrical twisting spiral. Backbone inside R groups outwards  ii) b-pleated sheet: several polypeptide segments lie side by side o many H-bonds extend from one part of chain to other.  Tertiary Structure:  Conformation of entire protein (3D)  Results from intramolecular interactions  Between R groups in the same chains  Observed with X-ray crystallography  2 TYPES - Fibrous Proteins:  Van der Waals forces = hydrophobic interactions  Hydrogen bonds  Ionic bonds  long strands or flattened sheets that resist pulling or shearing forces  eg. Collagens & elastins of ECM, keratins (hair, skin, fingernails), silk  structural materials - Globular Proteins:  Compact shape  Chains folded and twisted into complex shapes  Eg MOST PROTEINS  How do proteins fold? - While some proteins fold by a process of simple self- assembly, most proteins need some help. Chaperone proteins. Eg Hsp70 Chaperonin  Posttranslational Modifications: - After folding: proteins may be modified. - Cleaved: into smaller polypeptides - Sugar added to form glycoproteins - Metal/ion added to allow function  Protein domains ( alpha and beta domains): - Proteins have distinct domains (modules) that function in a semi-independent fashion - Bind different things or move independently of one another - Allows unique protein activities  Quaternary Structure:  linking of polypeptide chains to form multi subunit proteins - by intermolecular R Group interactions  May be linked by disulfide bonds, but more often non-covalent bonds (hydrophobic, H bonds, etc.) ie. hydrophobic patches on complementary amino acid of neighbouring polypeptides Cells: Rayana Alawie  Multiprotein Complexes: - Eg : Homodimer (2 identical proteins interacting together) and Heterodimer - different proteins, each with a specific function, become physically associated to form a much larger complex: some associations are stable and some are not - Often interactions between proteins regulated by changes eg. Phosphate addition  Insulin: - Small protein of 51 a.a - Cleaved into 2 polypeptides of 21 and 30 a.a into A and B- chain - Discovered by Banting and Best in 1923 ( Nobel Prize) -  How does it Bind? - Binds to insulin receptors to bring signal throughout the cell - binding of receptor to ligand via specific R-groups, causes conformational change in cytosolic portion of receptor - reveals kinase binding domain in receptor and kinase now binds transiently and phosphorylates receptor - phosphorylated receptor now can bind stably to another protein - this protein now acts as a docking site for cytoskeletal proteins to polymerize into multi-protein complexes CHAPTER 3: - How do we study cells? o Cell Culture: 1. Cell culture often forms the course material for the study of the cell biology 2. Allows us to study cells in a controlled in vitro system: cells grow in plastic flasks in special tissue culture media 3. Why use cell culture:  Cultured cells can be obtained in large quantity  Most cultures contain only a single type of cell  Wide variety of different cells can be grown in culture  Many different cellular activities can be studied  Chance to study cell differentiation  Cultured cells respond to treatment with drugs, hormones, growth factors and other active substances o Microscopy: 1. Optical microscopy  Bright-field microscopy: o condenser converges light on specimen forming bright light cone that enters objective; cone seen as bright background against which image of specimen is contrasted Cells: Rayana Alawie o Ideally suited for high contrast specimens (stained tissue sections); not good for all specimens o May not provide optimal visibility for other specimens o Preparation of Slides (BF):  Visualizing cells: Disadvantages  Fix cells : U have to kill cells.  Stain cells: to provide contrast  Mount on slides  Tissues: embed and section first. No 3D shape  Phase-contrast (P-C) microscopy + Different interference contrast (DIC) microscopy o Want to increase contrast without staining o Use specialized optics to increase contrast o Good for small, unstained specimens like living cells & those that are hard to
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